diff --git a/config/BUILD.bazel b/config/BUILD.bazel
index 0c95044..84c243f 100644
--- a/config/BUILD.bazel
+++ b/config/BUILD.bazel
@@ -1,4 +1,4 @@
-load("@rules_go//go:def.bzl", "go_library")
+load("@rules_go//go:def.bzl", "go_library", "go_test")
 
 go_library(
     name = "config",
@@ -12,3 +12,10 @@ go_library(
     visibility = ["//visibility:public"],
     deps = ["@com_github_goccy_go_yaml//:go-yaml"],
 )
+
+go_test(
+    name = "config_test",
+    srcs = ["config_test.go"],
+    embed = [":config"],
+    deps = ["@com_github_stretchr_testify//require"],
+)
diff --git a/config/config.go b/config/config.go
index 77ca493..41decb7 100644
--- a/config/config.go
+++ b/config/config.go
@@ -70,12 +70,24 @@ func Parse(configFilePath string) (*Config, error) {
 	if config.Service.WorkerPoolSize <= 0 {
 		return nil, fmt.Errorf("service.worker_pool_size must be > 0, got %d", config.Service.WorkerPoolSize)
 	}
+	if config.Service.Chunking.TargetChunkSize <= 0 {
+		return nil, fmt.Errorf("service.chunking.target_chunk_size must be > 0, got %d", config.Service.Chunking.TargetChunkSize)
+	}
+	if config.Service.Chunking.ChangedTargetChunkSize <= 0 {
+		return nil, fmt.Errorf("service.chunking.changed_target_chunk_size must be > 0, got %d", config.Service.Chunking.ChangedTargetChunkSize)
+	}
+	if config.Service.Chunking.MetadataMapChunkSize <= 0 {
+		return nil, fmt.Errorf("service.chunking.metadata_map_chunk_size must be > 0, got %d", config.Service.Chunking.MetadataMapChunkSize)
+	}
 	config.repositoryByRemote = make(map[string]*RepositoryConfig, len(config.Repository))
 	for i := range config.Repository {
 		remote := config.Repository[i].Remote
 		if remote == "" {
 			return nil, fmt.Errorf("repository[%d].remote must not be empty", i)
 		}
+		if config.Repository[i].QueryTimeoutSeconds <= 0 {
+			return nil, fmt.Errorf("repository[%d].query_timeout_seconds must be > 0", i)
+		}
 		if _, exists := config.repositoryByRemote[remote]; exists {
 			return nil, fmt.Errorf("duplicate repository remote %q", remote)
 		}
diff --git a/config/config_test.go b/config/config_test.go
new file mode 100644
index 0000000..eff9be6
--- /dev/null
+++ b/config/config_test.go
@@ -0,0 +1,186 @@
+// Copyright (c) 2025 Uber Technologies, Inc.
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+package config
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+
+	"github.com/stretchr/testify/require"
+)
+
+func TestParse_Validation(t *testing.T) {
+	t.Parallel()
+
+	validConfig := `
+repository:
+  - remote: "git@github.com:org/repo"
+    query_timeout_seconds: 300
+storage:
+  type: memory
+service:
+  worker_pool_size: 5
+  repo_manager_clone_path: /tmp/tango
+  chunking:
+    target_chunk_size: 250
+    changed_target_chunk_size: 125
+    metadata_map_chunk_size: 50000
+`
+
+	tests := []struct {
+		name    string
+		yaml    string
+		wantErr bool
+	}{
+		{
+			name: "valid config",
+			yaml: validConfig,
+		},
+		{
+			name: "worker_pool_size not set",
+			yaml: `
+repository:
+  - remote: "git@github.com:org/repo"
+    query_timeout_seconds: 300
+service:
+  chunking:
+    target_chunk_size: 250
+    changed_target_chunk_size: 125
+    metadata_map_chunk_size: 50000
+`,
+			wantErr: true,
+		},
+		{
+			name: "target_chunk_size not set",
+			yaml: `
+repository:
+  - remote: "git@github.com:org/repo"
+    query_timeout_seconds: 300
+service:
+  worker_pool_size: 5
+  chunking:
+    changed_target_chunk_size: 125
+    metadata_map_chunk_size: 50000
+`,
+			wantErr: true,
+		},
+		{
+			name: "changed_target_chunk_size not set",
+			yaml: `
+repository:
+  - remote: "git@github.com:org/repo"
+    query_timeout_seconds: 300
+service:
+  worker_pool_size: 5
+  chunking:
+    target_chunk_size: 250
+    metadata_map_chunk_size: 50000
+`,
+			wantErr: true,
+		},
+		{
+			name: "metadata_map_chunk_size not set",
+			yaml: `
+repository:
+  - remote: "git@github.com:org/repo"
+    query_timeout_seconds: 300
+service:
+  worker_pool_size: 5
+  chunking:
+    target_chunk_size: 250
+    changed_target_chunk_size: 125
+`,
+			wantErr: true,
+		},
+		{
+			name: "repository remote not set",
+			yaml: `
+repository:
+  - query_timeout_seconds: 300
+service:
+  worker_pool_size: 5
+  chunking:
+    target_chunk_size: 250
+    changed_target_chunk_size: 125
+    metadata_map_chunk_size: 50000
+`,
+			wantErr: true,
+		},
+		{
+			name: "query_timeout_seconds not set",
+			yaml: `
+repository:
+  - remote: "git@github.com:org/repo"
+service:
+  worker_pool_size: 5
+  chunking:
+    target_chunk_size: 250
+    changed_target_chunk_size: 125
+    metadata_map_chunk_size: 50000
+`,
+			wantErr: true,
+		},
+		{
+			name: "duplicate repository remote",
+			yaml: `
+repository:
+  - remote: "git@github.com:org/repo"
+    query_timeout_seconds: 300
+  - remote: "git@github.com:org/repo"
+    query_timeout_seconds: 300
+service:
+  worker_pool_size: 5
+  chunking:
+    target_chunk_size: 250
+    changed_target_chunk_size: 125
+    metadata_map_chunk_size: 50000
+`,
+			wantErr: true,
+		},
+		{
+			name: "worker_root_path without repo_manager_clone_path",
+			yaml: `
+repository:
+  - remote: "git@github.com:org/repo"
+    query_timeout_seconds: 300
+service:
+  worker_pool_size: 5
+  worker_root_path: /tmp/workers
+  chunking:
+    target_chunk_size: 250
+    changed_target_chunk_size: 125
+    metadata_map_chunk_size: 50000
+`,
+			wantErr: true,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			t.Parallel()
+			path := filepath.Join(t.TempDir(), "config.yaml")
+			require.NoError(t, os.WriteFile(path, []byte(tt.yaml), 0o644))
+
+			cfg, err := Parse(path)
+			if tt.wantErr {
+				require.Error(t, err, "expected error when %s", tt.name)
+			} else {
+				require.NoError(t, err)
+				require.NotNil(t, cfg)
+			}
+		})
+	}
+}
diff --git a/config/repository_config.go b/config/repository_config.go
index 4052ec4..8e23f0a 100644
--- a/config/repository_config.go
+++ b/config/repository_config.go
@@ -22,7 +22,7 @@ type RepositoryConfig struct {
 	ExcludeExternalTargets bool     `yaml:"exclude_external_targets"`
 	BzlmodEnabled          bool     `yaml:"bzlmod_enabled"`
 	BazelCommand           string   `yaml:"bazel_command"`
-	QueryTimeout           int64    `yaml:"query_timeout"` // in seconds
+	QueryTimeoutSeconds    int64    `yaml:"query_timeout_seconds"`
 	BazelExtraArgs         []string `yaml:"bazel_extra_args"`
 	StreamBazelLogs        bool     `yaml:"stream_bazel_logs"`
 }
diff --git a/controller/BUILD.bazel b/controller/BUILD.bazel
index 581ba3b..2194182 100644
--- a/controller/BUILD.bazel
+++ b/controller/BUILD.bazel
@@ -33,10 +33,10 @@ go_test(
         "getchangedtargets_test.go",
         "gettargetgraph_test.go",
         "output_filter_test.go",
-        "testhelper_test.go",
     ],
     embed = [":controller"],
     deps = [
+        "//config",
         "//core/common",
         "//core/storage",
         "//core/storage/storagemock",
@@ -46,7 +46,6 @@ go_test(
         "@com_github_gogo_protobuf//io",
         "@com_github_stretchr_testify//assert",
         "@com_github_stretchr_testify//require",
-        "@com_github_uber_go_tally//:tally",
         "@org_uber_go_mock//gomock",
         "@org_uber_go_zap//:zap",
         "@org_uber_go_zap//zaptest",
diff --git a/controller/controller.go b/controller/controller.go
index 34ca33c..92089c9 100644
--- a/controller/controller.go
+++ b/controller/controller.go
@@ -16,11 +16,11 @@ package controller
 
 import (
 	"context"
+	"fmt"
 	"time"
 
 	"github.com/uber-go/tally"
 	"github.com/uber/tango/config"
-	"github.com/uber/tango/core/common"
 	"github.com/uber/tango/core/storage"
 	"github.com/uber/tango/orchestrator"
 	pb "github.com/uber/tango/tangopb"
@@ -59,34 +59,31 @@ type controller struct {
 
 // NewController creates a new controller. appCtx is cancelled on process
 // shutdown to abort background work.
-func NewController(appCtx context.Context, p Params) pb.TangoYARPCServer {
+func NewController(appCtx context.Context, p Params) (pb.TangoYARPCServer, error) {
 	scope := p.Scope
 	if scope == nil {
 		scope = tally.NoopScope
 	}
-	targetChunkSize := p.ChunkConfig.TargetChunkSize
-	if targetChunkSize <= 0 {
-		targetChunkSize = common.DefaultTargetChunkSize
+	if p.ChunkConfig.TargetChunkSize <= 0 {
+		return nil, fmt.Errorf("target_chunk_size must be > 0, got %d", p.ChunkConfig.TargetChunkSize)
 	}
-	changedTargetChunkSize := p.ChunkConfig.ChangedTargetChunkSize
-	if changedTargetChunkSize <= 0 {
-		changedTargetChunkSize = common.DefaultChangedTargetChunkSize
+	if p.ChunkConfig.ChangedTargetChunkSize <= 0 {
+		return nil, fmt.Errorf("changed_target_chunk_size must be > 0, got %d", p.ChunkConfig.ChangedTargetChunkSize)
 	}
-	metadataMapChunkSize := p.ChunkConfig.MetadataMapChunkSize
-	if metadataMapChunkSize <= 0 {
-		metadataMapChunkSize = common.DefaultMetadataMapChunkSize
+	if p.ChunkConfig.MetadataMapChunkSize <= 0 {
+		return nil, fmt.Errorf("metadata_map_chunk_size must be > 0, got %d", p.ChunkConfig.MetadataMapChunkSize)
 	}
 	return &controller{
 		logger:                 p.Logger,
 		storage:                p.Storage,
 		orchestrator:           p.Orchestrator,
 		scope:                  scope.SubScope("controller"),
-		targetChunkSize:        targetChunkSize,
-		changedTargetChunkSize: changedTargetChunkSize,
-		metadataMapChunkSize:   metadataMapChunkSize,
+		targetChunkSize:        p.ChunkConfig.TargetChunkSize,
+		changedTargetChunkSize: p.ChunkConfig.ChangedTargetChunkSize,
+		metadataMapChunkSize:   p.ChunkConfig.MetadataMapChunkSize,
 		totalDurationBuckets:   _totalDurationBuckets,
 		appCtx:                 appCtx,
-	}
+	}, nil
 }
 
 // linkRequestCtx returns a context derived from reqCtx that is also cancelled
diff --git a/controller/controller_test.go b/controller/controller_test.go
index b891f87..c591866 100644
--- a/controller/controller_test.go
+++ b/controller/controller_test.go
@@ -19,11 +19,26 @@ import (
 	"testing"
 
 	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+	"github.com/uber/tango/config"
 	orchestratormock "github.com/uber/tango/orchestrator/orchestratormock"
 	"go.uber.org/mock/gomock"
 	"go.uber.org/zap"
 )
 
+var _testChunkConfig = config.ChunkConfig{
+	TargetChunkSize:        250,
+	ChangedTargetChunkSize: 125,
+	MetadataMapChunkSize:   50_000,
+}
+
+func newTestController(t *testing.T, appCtx context.Context, p Params) *controller {
+	t.Helper()
+	ctrl, err := NewController(appCtx, p)
+	require.NoError(t, err)
+	return ctrl.(*controller)
+}
+
 // TestNewController_StoresAppContext verifies the caller-supplied context is
 // retained and is the one observed by background goroutines.
 func TestNewController_StoresAppContext(t *testing.T) {
@@ -31,10 +46,11 @@ func TestNewController_StoresAppContext(t *testing.T) {
 	appCtx, cancel := context.WithCancel(context.Background())
 	defer cancel()
 
-	c := NewController(appCtx, Params{
+	c := newTestController(t, appCtx, Params{
 		Logger:       zap.NewNop(),
 		Orchestrator: orchestratormock.NewMockOrchestrator(ctrl),
-	}).(*controller)
+		ChunkConfig:  _testChunkConfig,
+	})
 
 	assert.Same(t, appCtx, c.appCtx)
 	assert.NoError(t, c.appCtx.Err())
@@ -101,3 +117,54 @@ func TestLinkRequestCtx_CancelReleasesAfterFunc(t *testing.T) {
 	cancelApp()
 	assert.Equal(t, firstErr, linked.Err(), "linked.Err() must not change after cancelLink")
 }
+
+func TestNewController_Validation(t *testing.T) {
+	t.Parallel()
+
+	valid := config.ChunkConfig{
+		TargetChunkSize:        250,
+		ChangedTargetChunkSize: 125,
+		MetadataMapChunkSize:   50_000,
+	}
+
+	tests := []struct {
+		name    string
+		chunk   config.ChunkConfig
+		wantErr bool
+	}{
+		{
+			name:  "valid",
+			chunk: valid,
+		},
+		{
+			name:    "target_chunk_size not set",
+			chunk:   config.ChunkConfig{ChangedTargetChunkSize: 125, MetadataMapChunkSize: 50_000},
+			wantErr: true,
+		},
+		{
+			name:    "changed_target_chunk_size not set",
+			chunk:   config.ChunkConfig{TargetChunkSize: 250, MetadataMapChunkSize: 50_000},
+			wantErr: true,
+		},
+		{
+			name:    "metadata_map_chunk_size not set",
+			chunk:   config.ChunkConfig{TargetChunkSize: 250, ChangedTargetChunkSize: 125},
+			wantErr: true,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			t.Parallel()
+			_, err := NewController(context.Background(), Params{
+				Logger:      zap.NewNop(),
+				ChunkConfig: tt.chunk,
+			})
+			if tt.wantErr {
+				require.Error(t, err, "expected error when %s", tt.name)
+			} else {
+				require.NoError(t, err)
+			}
+		})
+	}
+}
diff --git a/controller/getchangedtargets_test.go b/controller/getchangedtargets_test.go
index 1e854fc..02dda25 100644
--- a/controller/getchangedtargets_test.go
+++ b/controller/getchangedtargets_test.go
@@ -133,7 +133,7 @@ func TestValidateGetChangedTargetsRequest(t *testing.T) {
 }
 
 func TestCompareTargetGraphs(t *testing.T) {
-	c := newTestController(zap.NewNop())
+	c := newTestController(t, context.Background(), Params{Logger: zap.NewNop(), ChunkConfig: _testChunkConfig})
 
 	firstGraph := &pb.GetTargetGraphResponse{
 		Item: &pb.GetTargetGraphResponse_Metadata{
@@ -155,7 +155,11 @@ func TestGetChangedTargets_ValidationError(t *testing.T) {
 	ctrl := gomock.NewController(t)
 	stream := tangomock.NewMockTangoServiceGetChangedTargetsYARPCServer(ctrl)
 
-	c := NewController(context.Background(), Params{Logger: zap.NewNop(), Orchestrator: orchestratormock.NewMockOrchestrator(ctrl)})
+	c := newTestController(t, context.Background(), Params{
+		Logger:       zap.NewNop(),
+		Orchestrator: orchestratormock.NewMockOrchestrator(ctrl),
+		ChunkConfig:  _testChunkConfig,
+	})
 
 	err := c.GetChangedTargets(nil, stream)
 	assert.EqualError(t, err, "request cannot be nil")
@@ -196,10 +200,11 @@ func TestGetChangedTargets_CacheHit(t *testing.T) {
 
 	stream.EXPECT().Send(gomock.Any()).Return(nil).Times(2)
 
-	c := NewController(context.Background(), Params{
+	c := newTestController(t, context.Background(), Params{
 		Logger:       zaptest.NewLogger(t),
 		Storage:      storagemock,
 		Orchestrator: orchestratormock.NewMockOrchestrator(ctrl),
+		ChunkConfig:  _testChunkConfig,
 	})
 
 	request := &pb.GetChangedTargetsRequest{
@@ -227,10 +232,11 @@ func TestGetChangedTargets_TreehashReadError(t *testing.T) {
 	storagemock.EXPECT().Get(gomock.Any(), gomock.Any()).
 		Return(storage.DownloadResponse{}, injected).Times(2)
 
-	c := NewController(context.Background(), Params{
+	c := newTestController(t, context.Background(), Params{
 		Logger:       zap.NewNop(),
 		Storage:      storagemock,
 		Orchestrator: orchestratormock.NewMockOrchestrator(ctrl),
+		ChunkConfig:  _testChunkConfig,
 	})
 
 	request := &pb.GetChangedTargetsRequest{
@@ -316,10 +322,11 @@ func TestGetChangedTargets_StreamSendError(t *testing.T) {
 		return nil
 	})
 
-	c := NewController(context.Background(), Params{
+	c := newTestController(t, context.Background(), Params{
 		Logger:       zaptest.NewLogger(t),
 		Storage:      storagemock,
 		Orchestrator: orchestratormock.NewMockOrchestrator(ctrl),
+		ChunkConfig:  _testChunkConfig,
 	})
 
 	request := &pb.GetChangedTargetsRequest{
@@ -423,10 +430,11 @@ func TestGetChangedTargets_streamChunks(t *testing.T) {
 		return nil
 	})
 
-	c := NewController(context.Background(), Params{
+	c := newTestController(t, context.Background(), Params{
 		Logger:       zaptest.NewLogger(t),
 		Storage:      storagemock,
 		Orchestrator: orchestratormock.NewMockOrchestrator(ctrl),
+		ChunkConfig:  _testChunkConfig,
 	})
 
 	request := &pb.GetChangedTargetsRequest{
@@ -523,10 +531,11 @@ func TestGetChangedTargets_CacheWriteUsesAppCtx(t *testing.T) {
 
 	appCtx, cancelApp := context.WithCancel(context.Background())
 	defer cancelApp()
-	c := NewController(appCtx, Params{
+	c := newTestController(t, appCtx, Params{
 		Logger:       zaptest.NewLogger(t),
 		Storage:      storagemock,
 		Orchestrator: orchestratormock.NewMockOrchestrator(ctrl),
+		ChunkConfig:  _testChunkConfig,
 	})
 
 	request := &pb.GetChangedTargetsRequest{
@@ -576,7 +585,7 @@ func TestGetChangedTargets_CacheWriteUsesAppCtx(t *testing.T) {
 }
 
 func TestCompareTargetGraphs_NewTarget_CanonicalIDs(t *testing.T) {
-	c := newTestController(zaptest.NewLogger(t))
+	c := newTestController(t, context.Background(), Params{Logger: zaptest.NewLogger(t), ChunkConfig: _testChunkConfig})
 
 	first := []*pb.GetTargetGraphResponse{
 		{
@@ -629,7 +638,7 @@ func TestCompareTargetGraphs_NewTarget_CanonicalIDs(t *testing.T) {
 }
 
 func TestCompareTargetGraphs_SourceFileDirectAndPropagation(t *testing.T) {
-	c := newTestController(zaptest.NewLogger(t))
+	c := newTestController(t, context.Background(), Params{Logger: zaptest.NewLogger(t), ChunkConfig: _testChunkConfig})
 
 	// Old: source file A (id 1, hash h1), lib L (id 2, hash h1, dep -> A)
 	first := []*pb.GetTargetGraphResponse{
@@ -713,7 +722,7 @@ func TestCompareTargetGraphs_SourceFileDirectAndPropagation(t *testing.T) {
 }
 
 func TestCompareTargetGraphs_ChangedRuleUnreachableFromAnySeed(t *testing.T) {
-	c := newTestController(zaptest.NewLogger(t))
+	c := newTestController(t, context.Background(), Params{Logger: zaptest.NewLogger(t), ChunkConfig: _testChunkConfig})
 
 	// Old: T (id 1, rule), no deps
 	first := []*pb.GetTargetGraphResponse{
@@ -769,7 +778,7 @@ func TestCompareTargetGraphs_ChangedRuleUnreachableFromAnySeed(t *testing.T) {
 }
 
 func TestCompareTargetGraphs_ChangedWhenDependenciesChanged(t *testing.T) {
-	c := newTestController(zaptest.NewLogger(t))
+	c := newTestController(t, context.Background(), Params{Logger: zaptest.NewLogger(t), ChunkConfig: _testChunkConfig})
 
 	// Old: T (id 1, rule) with deps on A
 	first := []*pb.GetTargetGraphResponse{
@@ -845,7 +854,7 @@ func TestCompareTargetGraphs_ChangedWhenDependenciesChanged(t *testing.T) {
 }
 
 func TestCompareTargetGraphs_ChangedWhenAttributesChanged(t *testing.T) {
-	c := newTestController(zaptest.NewLogger(t))
+	c := newTestController(t, context.Background(), Params{Logger: zaptest.NewLogger(t), ChunkConfig: _testChunkConfig})
 
 	// Old: T with attribute "key1" -> "value1"
 	first := []*pb.GetTargetGraphResponse{
@@ -918,7 +927,7 @@ func TestCompareTargetGraphs_ChangedWhenAttributesChanged(t *testing.T) {
 }
 
 func TestCompareTargetGraphs_ChangedWhenNewAttributeAdded(t *testing.T) {
-	c := newTestController(zaptest.NewLogger(t))
+	c := newTestController(t, context.Background(), Params{Logger: zaptest.NewLogger(t), ChunkConfig: _testChunkConfig})
 
 	// Old: T with one attribute
 	first := []*pb.GetTargetGraphResponse{
@@ -1159,10 +1168,11 @@ func TestGetChangedTargets_CacheHitWithDistanceFilter(t *testing.T) {
 		return nil
 	}).Times(2)
 
-	c := NewController(context.Background(), Params{
+	c := newTestController(t, context.Background(), Params{
 		Logger:       zaptest.NewLogger(t),
 		Storage:      storagemock,
 		Orchestrator: orchestratormock.NewMockOrchestrator(ctrl),
+		ChunkConfig:  _testChunkConfig,
 	})
 
 	request := &pb.GetChangedTargetsRequest{
@@ -1256,7 +1266,7 @@ func TestComputeDistances_NilMetadata(t *testing.T) {
 }
 
 func TestCompareTargetGraphs_HashOnlyChangePropagatesViaBFS(t *testing.T) {
-	c := newTestController(zaptest.NewLogger(t))
+	c := newTestController(t, context.Background(), Params{Logger: zaptest.NewLogger(t), ChunkConfig: _testChunkConfig})
 
 	// Old: T (rule) with deps on source file A (id 10) and attributes
 	first := []*pb.GetTargetGraphResponse{
@@ -1349,7 +1359,7 @@ func TestCompareTargetGraphs_HashOnlyChangePropagatesViaBFS(t *testing.T) {
 }
 
 func TestCompareTargetGraphs_SiblingRuleNotPromotedToSeed(t *testing.T) {
-	c := newTestController(zaptest.NewLogger(t))
+	c := newTestController(t, context.Background(), Params{Logger: zaptest.NewLogger(t), ChunkConfig: _testChunkConfig})
 
 	// Source file A (id 1) owned by rule L (id 2).
 	// Rule T (id 3) depends on L (sibling rule), NOT directly on A.
@@ -1428,7 +1438,7 @@ func TestCompareTargetGraphs_SiblingRuleNotPromotedToSeed(t *testing.T) {
 }
 
 func TestCompareTargetGraphs_DeletedTargetEmitted(t *testing.T) {
-	c := newTestController(zaptest.NewLogger(t))
+	c := newTestController(t, context.Background(), Params{Logger: zaptest.NewLogger(t), ChunkConfig: _testChunkConfig})
 
 	// Old: T (rule) exists; New: T is gone.
 	first := []*pb.GetTargetGraphResponse{
diff --git a/controller/gettargetgraph_test.go b/controller/gettargetgraph_test.go
index e62856f..ed55bd8 100644
--- a/controller/gettargetgraph_test.go
+++ b/controller/gettargetgraph_test.go
@@ -46,9 +46,10 @@ func TestGetTargetGraph_CacheMiss_NoSend(t *testing.T) {
 		store.EXPECT().Get(gomock.Any(), gomock.Any()).
 			Return(storage.DownloadResponse{ReadCloser: newMockReadCloser([]byte{})}, nil),
 	)
-	c := NewController(context.Background(), Params{
-		Logger:  zaptest.NewLogger(t),
-		Storage: store,
+	c := newTestController(t, context.Background(), Params{
+		Logger:      zaptest.NewLogger(t),
+		Storage:     store,
+		ChunkConfig: _testChunkConfig,
 	})
 	req := &pb.GetTargetGraphRequest{
 		BuildDescription: &pb.BuildDescription{
@@ -71,9 +72,10 @@ func TestGetTargetGraph_StorageError_Propagates(t *testing.T) {
 	stream.EXPECT().Context().Return(context.Background())
 	storagemock := storagemock.NewMockStorage(ctrl)
 	storagemock.EXPECT().Get(gomock.Any(), gomock.Any()).Return(storage.DownloadResponse{}, expected)
-	c := NewController(context.Background(), Params{
-		Logger:  zaptest.NewLogger(t),
-		Storage: storagemock,
+	c := newTestController(t, context.Background(), Params{
+		Logger:      zaptest.NewLogger(t),
+		Storage:     storagemock,
+		ChunkConfig: _testChunkConfig,
 	})
 	err := c.GetTargetGraph(&pb.GetTargetGraphRequest{
 		BuildDescription: &pb.BuildDescription{
@@ -97,9 +99,10 @@ func TestGetTargetGraph_DecodeError_ReturnsError(t *testing.T) {
 		storagemock.EXPECT().Get(gomock.Any(), gomock.Any()).Return(storage.DownloadResponse{ReadCloser: newMockReadCloser([]byte("treehash-abc"))}, nil),
 		storagemock.EXPECT().Get(gomock.Any(), gomock.Any()).Return(storage.DownloadResponse{ReadCloser: newMockReadCloser([]byte("bad-bytes"))}, nil),
 	)
-	c := NewController(context.Background(), Params{
-		Logger:  zaptest.NewLogger(t),
-		Storage: storagemock,
+	c := newTestController(t, context.Background(), Params{
+		Logger:      zaptest.NewLogger(t),
+		Storage:     storagemock,
+		ChunkConfig: _testChunkConfig,
 	})
 	err := c.GetTargetGraph(&pb.GetTargetGraphRequest{
 		BuildDescription: &pb.BuildDescription{
@@ -130,9 +133,10 @@ func TestGetTargetGraph_SendsWhenItemPresent(t *testing.T) {
 		store.EXPECT().Get(gomock.Any(), gomock.Any()).Return(storage.DownloadResponse{ReadCloser: newMockReadCloser([]byte("treehash-xyz"))}, nil),
 		store.EXPECT().Get(gomock.Any(), gomock.Any()).Return(storage.DownloadResponse{ReadCloser: newMockReadCloser(buf.Bytes())}, nil),
 	)
-	c := NewController(context.Background(), Params{
-		Logger:  zaptest.NewLogger(t),
-		Storage: store,
+	c := newTestController(t, context.Background(), Params{
+		Logger:      zaptest.NewLogger(t),
+		Storage:     store,
+		ChunkConfig: _testChunkConfig,
 	})
 	err = c.GetTargetGraph(&pb.GetTargetGraphRequest{
 		BuildDescription: &pb.BuildDescription{
@@ -152,9 +156,10 @@ func TestGetTargetGraph_BuildDescriptionMissingRequiredFields_ReturnsError(t *te
 	stream := tangomock.NewMockTangoServiceGetTargetGraphYARPCServer(ctrl)
 	stream.EXPECT().Context().Return(context.Background())
 	store := storagemock.NewMockStorage(ctrl)
-	c := NewController(context.Background(), Params{
-		Logger:  zaptest.NewLogger(t),
-		Storage: store,
+	c := newTestController(t, context.Background(), Params{
+		Logger:      zaptest.NewLogger(t),
+		Storage:     store,
+		ChunkConfig: _testChunkConfig,
 	})
 	err := c.GetTargetGraph(&pb.GetTargetGraphRequest{
 		BuildDescription: &pb.BuildDescription{
@@ -173,9 +178,10 @@ func TestGetTargetGraph_MissingBuildDescription_ReturnsError(t *testing.T) {
 	stream := tangomock.NewMockTangoServiceGetTargetGraphYARPCServer(ctrl)
 	stream.EXPECT().Context().Return(context.Background())
 	store := storagemock.NewMockStorage(ctrl)
-	c := NewController(context.Background(), Params{
-		Logger:  zaptest.NewLogger(t),
-		Storage: store,
+	c := newTestController(t, context.Background(), Params{
+		Logger:      zaptest.NewLogger(t),
+		Storage:     store,
+		ChunkConfig: _testChunkConfig,
 	})
 	err := c.GetTargetGraph(&pb.GetTargetGraphRequest{}, stream)
 	assert.Error(t, err)
@@ -202,10 +208,11 @@ func TestGetTargetGraph_TreehashNotFound_NoError(t *testing.T) {
 	graphReader.EXPECT().Read().Return(nil, io.EOF).Times(1)
 	graphReader.EXPECT().Close().Return(nil)
 	orchestrator.EXPECT().GetTargetGraph(gomock.Any(), gomock.Any()).Return(graphReader, nil)
-	c := NewController(context.Background(), Params{
+	c := newTestController(t, context.Background(), Params{
 		Logger:       zaptest.NewLogger(t),
 		Storage:      store,
 		Orchestrator: orchestrator,
+		ChunkConfig:  _testChunkConfig,
 	})
 	err := c.GetTargetGraph(&pb.GetTargetGraphRequest{
 		BuildDescription: &pb.BuildDescription{Remote: "repo:go-code", BaseSha: "sha"},
@@ -220,9 +227,10 @@ func TestGetTargetGraph_TreehashReadError(t *testing.T) {
 	stream.EXPECT().Context().Return(context.Background())
 	store := storagemock.NewMockStorage(ctrl)
 	store.EXPECT().Get(gomock.Any(), gomock.Any()).Return(storage.DownloadResponse{ReadCloser: &errReadCloser{err: errors.New("readfail")}}, nil)
-	c := NewController(context.Background(), Params{
-		Logger:  zaptest.NewLogger(t),
-		Storage: store,
+	c := newTestController(t, context.Background(), Params{
+		Logger:      zaptest.NewLogger(t),
+		Storage:     store,
+		ChunkConfig: _testChunkConfig,
 	})
 	err := c.GetTargetGraph(&pb.GetTargetGraphRequest{
 		BuildDescription: &pb.BuildDescription{Remote: "repo:go-code", BaseSha: "sha"},
@@ -240,9 +248,10 @@ func TestGetTargetGraph_GraphFetchError(t *testing.T) {
 		store.EXPECT().Get(gomock.Any(), gomock.Any()).Return(storage.DownloadResponse{ReadCloser: newMockReadCloser([]byte("treehash-abc"))}, nil),
 		store.EXPECT().Get(gomock.Any(), gomock.Any()).Return(storage.DownloadResponse{}, errors.New("graph error")),
 	)
-	c := NewController(context.Background(), Params{
-		Logger:  zaptest.NewLogger(t),
-		Storage: store,
+	c := newTestController(t, context.Background(), Params{
+		Logger:      zaptest.NewLogger(t),
+		Storage:     store,
+		ChunkConfig: _testChunkConfig,
 	})
 	err := c.GetTargetGraph(&pb.GetTargetGraphRequest{
 		BuildDescription: &pb.BuildDescription{Remote: "repo:go-code", BaseSha: "sha"},
@@ -264,9 +273,10 @@ func TestGetTargetGraph_GraphReadError(t *testing.T) {
 		store.EXPECT().Get(gomock.Any(), gomock.Any()).Return(storage.DownloadResponse{ReadCloser: newMockReadCloser([]byte("treehash-abc"))}, nil),
 		store.EXPECT().Get(gomock.Any(), gomock.Any()).Return(storage.DownloadResponse{ReadCloser: &errReadCloser{err: errors.New("readfail")}}, nil),
 	)
-	c := NewController(context.Background(), Params{
-		Logger:  zaptest.NewLogger(t),
-		Storage: store,
+	c := newTestController(t, context.Background(), Params{
+		Logger:      zaptest.NewLogger(t),
+		Storage:     store,
+		ChunkConfig: _testChunkConfig,
 	})
 	err := c.GetTargetGraph(&pb.GetTargetGraphRequest{
 		BuildDescription: &pb.BuildDescription{Remote: "repo:go-code", BaseSha: "sha"},
@@ -292,9 +302,10 @@ func TestGetTargetGraph_StreamSendError(t *testing.T) {
 		storagemock.EXPECT().Get(gomock.Any(), gomock.Any()).Return(storage.DownloadResponse{ReadCloser: newMockReadCloser([]byte("treehash-abc"))}, nil),
 		storagemock.EXPECT().Get(gomock.Any(), gomock.Any()).Return(storage.DownloadResponse{ReadCloser: newMockReadCloser(buf.Bytes())}, nil),
 	)
-	c := NewController(context.Background(), Params{
-		Logger:  zaptest.NewLogger(t),
-		Storage: storagemock,
+	c := newTestController(t, context.Background(), Params{
+		Logger:      zaptest.NewLogger(t),
+		Storage:     storagemock,
+		ChunkConfig: _testChunkConfig,
 	})
 	err = c.GetTargetGraph(&pb.GetTargetGraphRequest{
 		BuildDescription: &pb.BuildDescription{Remote: "repo:go-code", BaseSha: "sha"},
@@ -321,10 +332,11 @@ func TestGetTargetGraph_GraphNotFound_FallsThrough(t *testing.T) {
 	graphReader.EXPECT().Read().Return(nil, io.EOF).Times(1)
 	graphReader.EXPECT().Close().Return(nil)
 	orch.EXPECT().GetTargetGraph(gomock.Any(), gomock.Any()).Return(graphReader, nil)
-	c := NewController(context.Background(), Params{
+	c := newTestController(t, context.Background(), Params{
 		Logger:       zaptest.NewLogger(t),
 		Storage:      store,
 		Orchestrator: orch,
+		ChunkConfig:  _testChunkConfig,
 	})
 	err := c.GetTargetGraph(&pb.GetTargetGraphRequest{
 		BuildDescription: &pb.BuildDescription{Remote: "repo:go-code", BaseSha: "sha"},
@@ -343,9 +355,10 @@ func TestGetTargetGraph_GraphReadCancelled(t *testing.T) {
 		store.EXPECT().Get(gomock.Any(), gomock.Any()).Return(storage.DownloadResponse{ReadCloser: newMockReadCloser([]byte("treehash-abc"))}, nil),
 		store.EXPECT().Get(gomock.Any(), gomock.Any()).Return(storage.DownloadResponse{}, errors.New("context canceled")),
 	)
-	c := NewController(context.Background(), Params{
-		Logger:  zaptest.NewLogger(t),
-		Storage: store,
+	c := newTestController(t, context.Background(), Params{
+		Logger:      zaptest.NewLogger(t),
+		Storage:     store,
+		ChunkConfig: _testChunkConfig,
 	})
 	err := c.GetTargetGraph(&pb.GetTargetGraphRequest{
 		BuildDescription: &pb.BuildDescription{Remote: "repo:go-code", BaseSha: "sha"},
@@ -367,10 +380,11 @@ func TestGetTargetGraph_OrchestratorCancelled(t *testing.T) {
 	store.EXPECT().Get(gomock.Any(), gomock.Any()).Return(storage.DownloadResponse{}, &storage.NotFoundError{Path: "x"})
 	orch := orchestratormock.NewMockOrchestrator(ctrl)
 	orch.EXPECT().GetTargetGraph(gomock.Any(), gomock.Any()).Return(nil, errors.New("context canceled"))
-	c := NewController(context.Background(), Params{
+	c := newTestController(t, context.Background(), Params{
 		Logger:       zaptest.NewLogger(t),
 		Storage:      store,
 		Orchestrator: orch,
+		ChunkConfig:  _testChunkConfig,
 	})
 	err := c.GetTargetGraph(&pb.GetTargetGraphRequest{
 		BuildDescription: &pb.BuildDescription{Remote: "repo:go-code", BaseSha: "sha"},
diff --git a/controller/testhelper_test.go b/controller/testhelper_test.go
deleted file mode 100644
index 56ff439..0000000
--- a/controller/testhelper_test.go
+++ /dev/null
@@ -1,35 +0,0 @@
-// Copyright (c) 2026 Uber Technologies, Inc.
-//
-// Licensed under the Apache License, Version 2.0 (the "License");
-// you may not use this file except in compliance with the License.
-// You may obtain a copy of the License at
-//
-//     http://www.apache.org/licenses/LICENSE-2.0
-//
-// Unless required by applicable law or agreed to in writing, software
-// distributed under the License is distributed on an "AS IS" BASIS,
-// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-// See the License for the specific language governing permissions and
-// limitations under the License.
-
-package controller
-
-import (
-	"context"
-
-	"github.com/uber-go/tally"
-	"github.com/uber/tango/core/common"
-	"go.uber.org/zap"
-)
-
-func newTestController(logger *zap.Logger) *controller {
-	return &controller{
-		logger:                 logger,
-		scope:                  tally.NoopScope,
-		targetChunkSize:        common.DefaultTargetChunkSize,
-		changedTargetChunkSize: common.DefaultChangedTargetChunkSize,
-		metadataMapChunkSize:   common.DefaultMetadataMapChunkSize,
-		totalDurationBuckets:   _totalDurationBuckets,
-		appCtx:                 context.Background(),
-	}
-}
diff --git a/core/bazel/bazel.go b/core/bazel/bazel.go
index 217283a..033930e 100644
--- a/core/bazel/bazel.go
+++ b/core/bazel/bazel.go
@@ -30,11 +30,6 @@ import (
 	"go.uber.org/zap"
 )
 
-const (
-	// default query timeout if not provided in config
-	_queryTimeout = 15 * time.Minute
-)
-
 type QueryRequest struct {
 	Query          string
 	StartupOptions []string
@@ -84,8 +79,8 @@ func NewBazelClient(ctx context.Context, p Params) (*BazelClient, error) {
 		}
 	}
 	timeout := p.QueryTimeout
-	if timeout == 0 {
-		timeout = _queryTimeout
+	if timeout <= 0 {
+		return nil, fmt.Errorf("query timeout must be > 0, got %s", timeout)
 	}
 	bazelCommand, err := detectBazelExecutable(ctx, p.BazelCommand)
 	if err != nil {
diff --git a/core/bazel/bazel_test.go b/core/bazel/bazel_test.go
index c76342a..c5cf88b 100644
--- a/core/bazel/bazel_test.go
+++ b/core/bazel/bazel_test.go
@@ -18,6 +18,7 @@ import (
 	"context"
 	"os/exec"
 	"testing"
+	"time"
 
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
@@ -36,6 +37,7 @@ func TestNewBazelClient(t *testing.T) {
 				WorkspacePath: "/tmp/test",
 				EnvVarsMap:    map[string]string{"FOO": "bar"},
 				Logger:        zap.NewNop().Sugar(),
+				QueryTimeout:  5 * time.Minute,
 				ExecCommandContext: func(ctx context.Context, name string, arg ...string) commander {
 					return nil
 				},
@@ -48,6 +50,7 @@ func TestNewBazelClient(t *testing.T) {
 				WorkspacePath: "/tmp/test",
 				EnvVarsMap:    map[string]string{"FOO": "bar"},
 				Logger:        zap.NewNop().Sugar(),
+				QueryTimeout:  5 * time.Minute,
 			},
 		},
 	}
@@ -72,6 +75,7 @@ func TestNewBazelClient_WithNilExecCommand(t *testing.T) {
 		WorkspacePath: "/workspace",
 		EnvVarsMap:    map[string]string{"KEY": "value"},
 		Logger:        zap.NewNop().Sugar(),
+		QueryTimeout:  5 * time.Minute,
 	})
 	require.NoError(t, err)
 	require.NotNil(t, client)
@@ -84,3 +88,45 @@ func TestNewBazelClient_WithNilExecCommand(t *testing.T) {
 	assert.Equal(t, "/workspace", execCmd.Dir)
 	assert.Contains(t, execCmd.Env, "KEY=value")
 }
+
+func TestNewBazelClient_Validation(t *testing.T) {
+	t.Parallel()
+
+	tests := []struct {
+		name    string
+		timeout time.Duration
+		wantErr bool
+	}{
+		{
+			name:    "valid timeout",
+			timeout: 5 * time.Minute,
+		},
+		{
+			name:    "query timeout not set",
+			timeout: 0,
+			wantErr: true,
+		},
+		{
+			name:    "negative query timeout",
+			timeout: -1 * time.Second,
+			wantErr: true,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			t.Parallel()
+			_, err := NewBazelClient(context.Background(), Params{
+				BazelCommand:  "bazel",
+				WorkspacePath: "/tmp/test",
+				Logger:        zap.NewNop().Sugar(),
+				QueryTimeout:  tt.timeout,
+			})
+			if tt.wantErr {
+				require.Error(t, err, "expected error when %s", tt.name)
+			} else {
+				require.NoError(t, err)
+			}
+		})
+	}
+}
diff --git a/core/bazel/query_test.go b/core/bazel/query_test.go
index c506214..09337a8 100644
--- a/core/bazel/query_test.go
+++ b/core/bazel/query_test.go
@@ -57,6 +57,7 @@ func TestExecuteQuery_Success(t *testing.T) {
 		mockCmd.EXPECT().Wait().Return(nil),
 	)
 	client, err := NewBazelClient(context.Background(), Params{
+		QueryTimeout:  5 * time.Minute,
 		BazelCommand:  "bazel",
 		WorkspacePath: "/tmp/test",
 		EnvVarsMap:    map[string]string{},
@@ -101,6 +102,7 @@ func TestExecuteQuery_WithStartupOptions(t *testing.T) {
 		mockCmd.EXPECT().Wait().Return(nil),
 	)
 	client, err := NewBazelClient(context.Background(), Params{
+		QueryTimeout:  5 * time.Minute,
 		BazelCommand:  "bazel",
 		WorkspacePath: "/tmp/test",
 		EnvVarsMap:    map[string]string{},
@@ -230,6 +232,7 @@ func TestExecuteQueryInternal_Failures(t *testing.T) {
 			tt.setupMock(mockCmd)
 
 			client, err := NewBazelClient(context.Background(), Params{
+				QueryTimeout:  5 * time.Minute,
 				BazelCommand:  "bazel",
 				WorkspacePath: "/tmp/test",
 				EnvVarsMap:    map[string]string{},
@@ -259,6 +262,7 @@ func TestExecuteQuery_ErrorCase(t *testing.T) {
 	mockCmd.EXPECT().StdoutPipe().Return(nil, errors.New("stdout pipe failed"))
 
 	client, err := NewBazelClient(context.Background(), Params{
+		QueryTimeout:  5 * time.Minute,
 		BazelCommand:  "bazel",
 		WorkspacePath: "/tmp/test",
 		EnvVarsMap:    map[string]string{},
diff --git a/core/common/utils.go b/core/common/utils.go
index 90df802..e46a170 100644
--- a/core/common/utils.go
+++ b/core/common/utils.go
@@ -28,24 +28,6 @@ import (
 	"github.com/uber/tango/tangopb"
 )
 
-const (
-	// DefaultTargetChunkSize is the default number of OptimizedTarget entries per stream message.
-	// Sized conservatively: at ~40KB/target worst-case (target with ~10K direct deps × 4 bytes),
-	// 250 targets ≈ 10MB — well under the 64MB default gRPC per-message limit.
-	DefaultTargetChunkSize = 250
-
-	// DefaultChangedTargetChunkSize is the default number of ChangedTarget entries per stream message.
-	// A ChangedTarget carries both old_target and new_target (2× an OptimizedTarget), so we use
-	// half the regular chunk size to stay within the same byte budget.
-	DefaultChangedTargetChunkSize = 125
-
-	// DefaultMetadataMapChunkSize is the max entries per metadata message chunk.
-	// target_id_mapping and attribute_string_value_mapping scale with repo size and can exceed
-	// the 64MB gRPC message limit for large monorepos, so they are split across multiple messages.
-	// At ~85 bytes/entry (60-char avg target name + proto overhead), 50 000 entries ≈ 4.25MB per chunk.
-	DefaultMetadataMapChunkSize = 50_000
-)
-
 // ToShortRemote returns the short remote name given a git ssh remote string.
 // For example, "git@github:uber/tango" will return "uber/tango".
 func ToShortRemote(remote string) string {
@@ -137,8 +119,10 @@ func HashRequestOptions(opts *tangopb.RequestOptions) string {
 // for typical target rates.
 const cancelCheckInterval = 4096
 
-// ResultToGetTargetGraphResponse converts a Result to a GetTargetGraphResponse
-func ResultToGetTargetGraphResponse(ctx context.Context, result targethasher.Result) ([]*tangopb.GetTargetGraphResponse, error) {
+// ResultToGetTargetGraphResponse converts a Result to a GetTargetGraphResponse.
+// targetChunkSize controls how many OptimizedTarget entries per stream message.
+// metadataMapChunkSize controls how many entries per metadata map chunk.
+func ResultToGetTargetGraphResponse(ctx context.Context, result targethasher.Result, targetChunkSize, metadataMapChunkSize int) ([]*tangopb.GetTargetGraphResponse, error) {
 	// Map target names to ids. This list is topologically sorted, so the ids are stable.
 	// IDs start at 1 — 0 is reserved as the proto3 "unset" sentinel so consumers using
 	// encoding/json (which honors `omitempty` on int32 fields) never silently lose a target.
@@ -224,14 +208,14 @@ func ResultToGetTargetGraphResponse(ctx context.Context, result targethasher.Res
 	attrStrValIDToVal := attrStrValMapper.Invert()
 
 	// chunk targets into multiple messages for streaming
-	responses := chunkTargets(optimizedTargets, DefaultTargetChunkSize)
+	responses := chunkTargets(optimizedTargets, targetChunkSize)
 	for _, meta := range ChunkMetadata(
 		targetIDToName,
 		ruleTypeIDToName,
 		tagIDToName,
 		attrNameIDToName,
 		attrStrValIDToVal,
-		DefaultMetadataMapChunkSize,
+		metadataMapChunkSize,
 	) {
 		responses = append(responses, &tangopb.GetTargetGraphResponse{
 			Item: &tangopb.GetTargetGraphResponse_Metadata{Metadata: meta},
@@ -242,10 +226,6 @@ func ResultToGetTargetGraphResponse(ctx context.Context, result targethasher.Res
 }
 
 func chunkTargets(targets []*tangopb.OptimizedTarget, chunkSize int) []*tangopb.GetTargetGraphResponse {
-	if chunkSize <= 0 {
-		chunkSize = DefaultTargetChunkSize
-	}
-
 	// at least one chunk
 	numChunks := max(1, (len(targets)+chunkSize-1)/chunkSize)
 
@@ -293,10 +273,6 @@ func ChunkMetadata(
 	attrStrValIDToVal map[int32]string,
 	chunkSize int,
 ) []*tangopb.Metadata {
-	if chunkSize <= 0 {
-		chunkSize = DefaultMetadataMapChunkSize
-	}
-
 	targetChunks := splitMap(targetIDToName, chunkSize)
 	attrValChunks := splitMap(attrStrValIDToVal, chunkSize)
 
diff --git a/core/common/utils_test.go b/core/common/utils_test.go
index 4172da0..ea1ecd9 100644
--- a/core/common/utils_test.go
+++ b/core/common/utils_test.go
@@ -186,7 +186,7 @@ func TestChunkTargets(t *testing.T) {
 func TestResultToGetTargetGraphResponse_Chunking(t *testing.T) {
 	t.Parallel()
 
-	// 500 targets with DefaultTargetChunkSize=250 → 2 target chunks + 1 metadata = 3 responses
+	// 500 targets with targetChunkSize=250 → 2 target chunks + 1 metadata = 3 responses
 	numTargets := 500
 	result := targethasher.Result{
 		TargetNames: make([]string, numTargets),
@@ -198,10 +198,10 @@ func TestResultToGetTargetGraphResponse_Chunking(t *testing.T) {
 		result.Targets[name] = &targethasher.Target{Name: name, Hash: []byte{0}, RuleType: "go_library"}
 	}
 
-	responses, err := ResultToGetTargetGraphResponse(context.Background(), result)
+	responses, err := ResultToGetTargetGraphResponse(context.Background(), result, 250, 50_000)
 	require.NoError(t, err)
 
-	// 2 target chunks + 1 metadata chunk (500 targets well under DefaultMetadataMapChunkSize)
+	// 2 target chunks + 1 metadata chunk (500 targets well under metadataMapChunkSize)
 	require.Len(t, responses, 3)
 
 	for _, resp := range responses[:2] {
diff --git a/example/cmd/query-bench/main.go b/example/cmd/query-bench/main.go
index 3071b01..8efaa25 100644
--- a/example/cmd/query-bench/main.go
+++ b/example/cmd/query-bench/main.go
@@ -112,7 +112,7 @@ func run() error {
 		totalDuration += elapsed
 		fmt.Printf("run %d: targethasher: %v  (%d targets)\n", i+1, elapsed.Round(time.Millisecond), len(targethasherResult.TargetNames))
 		start = time.Now()
-		response, err := common.ResultToGetTargetGraphResponse(ctx, targethasherResult) // also print the time to convert to GetTargetGraphResponse format
+		response, err := common.ResultToGetTargetGraphResponse(ctx, targethasherResult, 250, 50_000)
 		if err != nil {
 			return fmt.Errorf("run %d: converting to GetTargetGraphResponse: %w", i+1, err)
 		}
diff --git a/example/main.go b/example/main.go
index 05a3036..c5c900d 100644
--- a/example/main.go
+++ b/example/main.go
@@ -105,11 +105,15 @@ func run() error {
 
 	// Controller (YARPC server implementation). appCtx is forwarded so the
 	// controller's background goroutines are tied to process lifetime.
-	ctrl := controller.NewController(appCtx, controller.Params{
+	ctrl, err := controller.NewController(appCtx, controller.Params{
 		Logger:       zl,
 		Storage:      store,
 		Orchestrator: orch,
+		ChunkConfig:  cfg.Service.Chunking,
 	})
+	if err != nil {
+		return fmt.Errorf("failed to create controller: %w", err)
+	}
 
 	// YARPC transports and dispatcher
 	grpcTransport := yarpcgrpc.NewTransport()
diff --git a/example/tango-config.yaml b/example/tango-config.yaml
index ec43e6a..8608c65 100644
--- a/example/tango-config.yaml
+++ b/example/tango-config.yaml
@@ -15,7 +15,7 @@ repository:
       - "^@@?bazel_tools/"
     exclude_external_targets: true
     bzlmod_enabled: true
-    query_timeout: 300
+    query_timeout_seconds: 300
 
 # Service configuration
 service:
@@ -24,3 +24,7 @@ service:
   repo_manager_clone_path: "/tmp/tango-repo-manager"
   # root for worker checkouts; defaults to repo_manager_clone_path/.workers
   worker_root_path: "/tmp/tango/workers"
+  chunking:
+    target_chunk_size: 250
+    changed_target_chunk_size: 125
+    metadata_map_chunk_size: 50000
diff --git a/orchestrator/native_orchestrator.go b/orchestrator/native_orchestrator.go
index f46c2ab..0f99272 100644
--- a/orchestrator/native_orchestrator.go
+++ b/orchestrator/native_orchestrator.go
@@ -187,7 +187,7 @@ func (b *nativeOrchestrator) GetTargetGraph(ctx context.Context, param GetTarget
 			WorkspacePath: ws.Path(),
 			Logger:        b.logger,
 			BazelCommand:  repoCfg.BazelCommand,
-			QueryTimeout:  time.Duration(repoCfg.QueryTimeout) * time.Second,
+			QueryTimeout:  time.Duration(repoCfg.QueryTimeoutSeconds) * time.Second,
 			StreamLogs:    repoCfg.StreamBazelLogs,
 		})
 		if err != nil {
@@ -206,7 +206,7 @@ func (b *nativeOrchestrator) GetTargetGraph(ctx context.Context, param GetTarget
 	if err != nil {
 		return nil, fmt.Errorf("compute target graph: %w", err)
 	}
-	responses, err := common.ResultToGetTargetGraphResponse(ctx, result)
+	responses, err := common.ResultToGetTargetGraphResponse(ctx, result, b.config.Service.Chunking.TargetChunkSize, b.config.Service.Chunking.MetadataMapChunkSize)
 	if err != nil {
 		return nil, fmt.Errorf("convert target graph to response: %w", err)
 	}
diff --git a/orchestrator/testdata/config.yaml b/orchestrator/testdata/config.yaml
index f420f74..2fc7793 100644
--- a/orchestrator/testdata/config.yaml
+++ b/orchestrator/testdata/config.yaml
@@ -7,7 +7,11 @@ repository:
       - "*.gen.go"
     exclude_external_targets: true
     bzlmod_enabled: true
-    query_timeout: 15
+    query_timeout_seconds: 15
 
 service:
   worker_pool_size: 3
+  chunking:
+    target_chunk_size: 250
+    changed_target_chunk_size: 125
+    metadata_map_chunk_size: 50000