diff --git a/github_ops_manager/configuration/cli.py b/github_ops_manager/configuration/cli.py
index b65d43a..46ff124 100644
--- a/github_ops_manager/configuration/cli.py
+++ b/github_ops_manager/configuration/cli.py
@@ -266,10 +266,14 @@ def process_test_requirements_cli(
     - Writing metadata back to test_cases.yaml files
 
     For each test case:
-    - If project_issue_number is missing, creates an issue
+    - If metadata.project_tracking.issue_number is missing, creates an issue
     - If generated_script_path exists and PR metadata is missing:
-      - Non-catalog: creates PR in project repo
-      - Catalog-destined: creates PR in catalog repo
+      - Non-catalog (metadata.catalog.destined != true): creates PR in project repo
+      - Catalog-destined (metadata.catalog.destined == true): creates PR in catalog repo
+
+    Metadata structure written:
+    - metadata.project_tracking.{issue_number, issue_url, pr_number, pr_url, pr_branch, git_url}
+    - metadata.catalog_tracking.{pr_number, pr_url, pr_branch, git_url}
 
     MIGRATION: If --issues-yaml is provided, existing metadata from issues.yaml
     will be migrated to test_cases.yaml before normal processing begins.
diff --git a/github_ops_manager/processing/test_cases_processor.py b/github_ops_manager/processing/test_cases_processor.py
index c28e300..b667bdf 100644
--- a/github_ops_manager/processing/test_cases_processor.py
+++ b/github_ops_manager/processing/test_cases_processor.py
@@ -14,6 +14,7 @@
 
 logger: structlog.stdlib.BoundLogger = structlog.get_logger(__name__)
 
+
 # Initialize YAML handler with format preservation
 yaml = YAML()
 yaml.preserve_quotes = True
@@ -254,7 +255,10 @@ def find_test_case_by_filename(test_cases: list[dict[str, Any]], generated_scrip
 
 
 def update_test_case_with_pr_metadata(test_case: dict[str, Any], pr: PullRequest, catalog_repo_url: str) -> dict[str, Any]:
-    """Add PR metadata fields to test case.
+    """Add catalog PR metadata fields to test case.
+
+    Writes metadata to the nested structure:
+        metadata.catalog_tracking.{pr_number, pr_url, pr_branch, git_url}
 
     Args:
         test_case: Test case dictionary to update
@@ -264,13 +268,14 @@ def update_test_case_with_pr_metadata(test_case: dict[str, Any], pr: PullRequest
     Returns:
         Updated test case dictionary
     """
-    test_case["catalog_pr_git_url"] = catalog_repo_url
-    test_case["catalog_pr_number"] = pr.number
-    test_case["catalog_pr_url"] = pr.html_url
-    test_case["catalog_pr_branch"] = pr.head.ref
+    catalog_tracking = test_case.setdefault("metadata", {}).setdefault("catalog_tracking", {})
+    catalog_tracking["git_url"] = catalog_repo_url
+    catalog_tracking["pr_number"] = pr.number
+    catalog_tracking["pr_url"] = pr.html_url
+    catalog_tracking["pr_branch"] = pr.head.ref
 
     logger.info(
-        "Updated test case with PR metadata",
+        "Updated test case with catalog PR metadata",
         catalog_pr_number=pr.number,
         catalog_pr_url=pr.html_url,
         catalog_pr_branch=pr.head.ref,
@@ -282,6 +287,9 @@ def update_test_case_with_pr_metadata(test_case: dict[str, Any], pr: PullRequest
 def update_test_case_with_issue_metadata(test_case: dict[str, Any], issue_number: int, issue_url: str) -> dict[str, Any]:
     """Add project issue metadata fields to test case.
 
+    Writes metadata to the nested structure:
+        metadata.project_tracking.{issue_number, issue_url}
+
     Args:
         test_case: Test case dictionary to update
         issue_number: GitHub Issue number
@@ -290,8 +298,9 @@ def update_test_case_with_issue_metadata(test_case: dict[str, Any], issue_number
     Returns:
         Updated test case dictionary
     """
-    test_case["project_issue_number"] = issue_number
-    test_case["project_issue_url"] = issue_url
+    project_tracking = test_case.setdefault("metadata", {}).setdefault("project_tracking", {})
+    project_tracking["issue_number"] = issue_number
+    project_tracking["issue_url"] = issue_url
 
     logger.info(
         "Updated test case with project issue metadata",
@@ -311,6 +320,9 @@ def update_test_case_with_project_pr_metadata(
 ) -> dict[str, Any]:
     """Add project PR metadata fields to test case.
 
+    Writes metadata to the nested structure:
+        metadata.project_tracking.{pr_number, pr_url, pr_branch, git_url}
+
     Args:
         test_case: Test case dictionary to update
         pr_number: GitHub Pull Request number
@@ -321,10 +333,11 @@ def update_test_case_with_project_pr_metadata(
     Returns:
         Updated test case dictionary
     """
-    test_case["project_pr_git_url"] = repo_url
-    test_case["project_pr_number"] = pr_number
-    test_case["project_pr_url"] = pr_url
-    test_case["project_pr_branch"] = pr_branch
+    project_tracking = test_case.setdefault("metadata", {}).setdefault("project_tracking", {})
+    project_tracking["git_url"] = repo_url
+    project_tracking["pr_number"] = pr_number
+    project_tracking["pr_url"] = pr_url
+    project_tracking["pr_branch"] = pr_branch
 
     logger.info(
         "Updated test case with project PR metadata",
@@ -340,6 +353,7 @@ def requires_issue_creation(test_case: dict[str, Any]) -> bool:
     """Check if a test case needs an issue to be created.
 
     An issue is needed if the test case doesn't already have issue metadata.
+    Checks nested structure: metadata.project_tracking.{issue_number, issue_url}
 
     Args:
         test_case: Test case dictionary to check
@@ -347,8 +361,9 @@ def requires_issue_creation(test_case: dict[str, Any]) -> bool:
     Returns:
         True if issue needs to be created, False otherwise
     """
-    has_issue_number = test_case.get("project_issue_number") is not None
-    has_issue_url = test_case.get("project_issue_url") is not None
+    project_tracking = test_case.get("metadata", {}).get("project_tracking", {})
+    has_issue_number = project_tracking.get("issue_number") is not None
+    has_issue_url = project_tracking.get("issue_url") is not None
 
     return not (has_issue_number and has_issue_url)
 
@@ -358,8 +373,9 @@ def requires_project_pr_creation(test_case: dict[str, Any]) -> bool:
 
     A project PR is needed if:
     - The test case has a generated_script_path (script exists)
-    - The test case is NOT catalog-destined
+    - The test case is NOT catalog-destined (metadata.catalog.destined)
     - The test case doesn't already have project PR metadata
+      (metadata.project_tracking.{pr_number, pr_url})
 
     Args:
         test_case: Test case dictionary to check
@@ -367,10 +383,12 @@ def requires_project_pr_creation(test_case: dict[str, Any]) -> bool:
     Returns:
         True if project PR needs to be created, False otherwise
     """
+    metadata = test_case.get("metadata", {})
     has_script = test_case.get("generated_script_path") is not None
-    is_catalog = test_case.get("catalog_destined", False)
-    has_pr_number = test_case.get("project_pr_number") is not None
-    has_pr_url = test_case.get("project_pr_url") is not None
+    is_catalog = metadata.get("catalog", {}).get("destined", False)
+    project_tracking = metadata.get("project_tracking", {})
+    has_pr_number = project_tracking.get("pr_number") is not None
+    has_pr_url = project_tracking.get("pr_url") is not None
 
     return has_script and not is_catalog and not (has_pr_number and has_pr_url)
 
@@ -380,8 +398,9 @@ def requires_catalog_pr_creation(test_case: dict[str, Any]) -> bool:
 
     A catalog PR is needed if:
     - The test case has a generated_script_path (script exists)
-    - The test case IS catalog-destined
+    - The test case IS catalog-destined (metadata.catalog.destined)
     - The test case doesn't already have catalog PR metadata
+      (metadata.catalog_tracking.{pr_number, pr_url})
 
     Args:
         test_case: Test case dictionary to check
@@ -389,10 +408,12 @@ def requires_catalog_pr_creation(test_case: dict[str, Any]) -> bool:
     Returns:
         True if catalog PR needs to be created, False otherwise
     """
+    metadata = test_case.get("metadata", {})
     has_script = test_case.get("generated_script_path") is not None
-    is_catalog = test_case.get("catalog_destined", False)
-    has_pr_number = test_case.get("catalog_pr_number") is not None
-    has_pr_url = test_case.get("catalog_pr_url") is not None
+    is_catalog = metadata.get("catalog", {}).get("destined", False)
+    catalog_tracking = metadata.get("catalog_tracking", {})
+    has_pr_number = catalog_tracking.get("pr_number") is not None
+    has_pr_url = catalog_tracking.get("pr_url") is not None
 
     return has_script and is_catalog and not (has_pr_number and has_pr_url)
 
@@ -400,11 +421,13 @@ def requires_catalog_pr_creation(test_case: dict[str, Any]) -> bool:
 def load_catalog_destined_test_cases(test_cases_dir: Path) -> list[dict[str, Any]]:
     """Load test cases that are catalog-destined from test_cases.yaml files.
 
+    Checks nested structure: metadata.catalog.destined
+
     Args:
         test_cases_dir: Directory containing test_cases.yaml files
 
     Returns:
-        List of test case dictionaries with catalog_destined=true
+        List of test case dictionaries with metadata.catalog.destined=true
     """
     catalog_test_cases = []
     test_case_files = find_test_cases_files(test_cases_dir)
@@ -421,7 +444,7 @@ def load_catalog_destined_test_cases(test_cases_dir: Path) -> list[dict[str, Any
 
         # Filter for catalog-destined test cases with generated scripts
         for test_case in test_cases:
-            is_catalog = test_case.get("catalog_destined", False)
+            is_catalog = test_case.get("metadata", {}).get("catalog", {}).get("destined", False)
             has_script = test_case.get("generated_script_path")
 
             if is_catalog and has_script:
@@ -470,7 +493,7 @@ def load_all_test_cases(test_cases_dir: Path) -> list[dict[str, Any]]:
             logger.debug(
                 "Loaded test case",
                 title=test_case.get("title"),
-                catalog_destined=test_case.get("catalog_destined", False),
+                catalog_destined=test_case.get("metadata", {}).get("catalog", {}).get("destined", False),
                 has_script=test_case.get("generated_script_path") is not None,
                 source_file=str(test_case_file),
             )
diff --git a/github_ops_manager/synchronize/pull_requests.py b/github_ops_manager/synchronize/pull_requests.py
index a141038..f88dd70 100644
--- a/github_ops_manager/synchronize/pull_requests.py
+++ b/github_ops_manager/synchronize/pull_requests.py
@@ -462,8 +462,9 @@ async def create_catalog_pull_requests(
         logger.info("Processing catalog test case", title=title, script_path=script_path)
 
         # Check if PR already exists
-        existing_pr_number = test_case.get("catalog_pr_number")
-        existing_pr_url = test_case.get("catalog_pr_url")
+        catalog_tracking = test_case.get("metadata", {}).get("catalog_tracking", {})
+        existing_pr_number = catalog_tracking.get("pr_number")
+        existing_pr_url = catalog_tracking.get("pr_url")
 
         if existing_pr_number and existing_pr_url:
             logger.info("PR already exists for test case, skipping", title=title, pr_number=existing_pr_number, pr_url=existing_pr_url)
diff --git a/github_ops_manager/synchronize/test_requirements.py b/github_ops_manager/synchronize/test_requirements.py
index 0bdcd53..11370b7 100644
--- a/github_ops_manager/synchronize/test_requirements.py
+++ b/github_ops_manager/synchronize/test_requirements.py
@@ -143,8 +143,9 @@ async def create_project_pr_for_test_case(
         pr_title = f"GenAI, Review: {title}"
 
         # Build PR body with issue reference if available
-        issue_number = test_case.get("project_issue_number")
-        issue_url = test_case.get("project_issue_url")
+        project_tracking = test_case.get("metadata", {}).get("project_tracking", {})
+        issue_number = project_tracking.get("issue_number")
+        issue_url = project_tracking.get("issue_url")
 
         if issue_number:
             pr_body = f"""**Quicksilver**: Automatically generated Pull Request for issue #{issue_number}.
diff --git a/tests/unit/test_processing_test_cases_processor.py b/tests/unit/test_processing_test_cases_processor.py
index 2617055..e02dba1 100644
--- a/tests/unit/test_processing_test_cases_processor.py
+++ b/tests/unit/test_processing_test_cases_processor.py
@@ -62,24 +62,28 @@ class TestUpdateTestCaseWithIssueMetadata:
     """Tests for update_test_case_with_issue_metadata function."""
 
     def test_adds_issue_metadata(self) -> None:
-        """Should add issue number and URL to test case."""
+        """Should add issue number and URL to test case in nested structure."""
         test_case: dict[str, Any] = {"title": "Test Case 1"}
         result = update_test_case_with_issue_metadata(test_case, 123, "https://github.com/org/repo/issues/123")
 
-        assert result["project_issue_number"] == 123
-        assert result["project_issue_url"] == "https://github.com/org/repo/issues/123"
+        assert result["metadata"]["project_tracking"]["issue_number"] == 123
+        assert result["metadata"]["project_tracking"]["issue_url"] == "https://github.com/org/repo/issues/123"
 
     def test_overwrites_existing_metadata(self) -> None:
         """Should overwrite existing issue metadata."""
         test_case: dict[str, Any] = {
             "title": "Test Case 1",
-            "project_issue_number": 100,
-            "project_issue_url": "https://old-url",
+            "metadata": {
+                "project_tracking": {
+                    "issue_number": 100,
+                    "issue_url": "https://old-url",
+                }
+            },
         }
         result = update_test_case_with_issue_metadata(test_case, 200, "https://new-url")
 
-        assert result["project_issue_number"] == 200
-        assert result["project_issue_url"] == "https://new-url"
+        assert result["metadata"]["project_tracking"]["issue_number"] == 200
+        assert result["metadata"]["project_tracking"]["issue_url"] == "https://new-url"
 
     def test_returns_same_dict(self) -> None:
         """Should return the same dictionary object (mutated in place)."""
@@ -93,7 +97,7 @@ class TestUpdateTestCaseWithProjectPrMetadata:
     """Tests for update_test_case_with_project_pr_metadata function."""
 
     def test_adds_project_pr_metadata(self) -> None:
-        """Should add all project PR metadata fields."""
+        """Should add all project PR metadata fields in nested structure."""
         test_case: dict[str, Any] = {"title": "Test Case 1"}
         result = update_test_case_with_project_pr_metadata(
             test_case,
@@ -103,17 +107,21 @@ def test_adds_project_pr_metadata(self) -> None:
             repo_url="https://github.com/org/repo",
         )
 
-        assert result["project_pr_number"] == 456
-        assert result["project_pr_url"] == "https://github.com/org/repo/pull/456"
-        assert result["project_pr_branch"] == "feature/test-case-1"
-        assert result["project_pr_git_url"] == "https://github.com/org/repo"
+        assert result["metadata"]["project_tracking"]["pr_number"] == 456
+        assert result["metadata"]["project_tracking"]["pr_url"] == "https://github.com/org/repo/pull/456"
+        assert result["metadata"]["project_tracking"]["pr_branch"] == "feature/test-case-1"
+        assert result["metadata"]["project_tracking"]["git_url"] == "https://github.com/org/repo"
 
     def test_overwrites_existing_metadata(self) -> None:
         """Should overwrite existing project PR metadata."""
         test_case: dict[str, Any] = {
             "title": "Test Case 1",
-            "project_pr_number": 100,
-            "project_pr_url": "https://old-url",
+            "metadata": {
+                "project_tracking": {
+                    "pr_number": 100,
+                    "pr_url": "https://old-url",
+                }
+            },
         }
         result = update_test_case_with_project_pr_metadata(
             test_case,
@@ -123,15 +131,15 @@ def test_overwrites_existing_metadata(self) -> None:
             repo_url="https://repo",
         )
 
-        assert result["project_pr_number"] == 200
-        assert result["project_pr_url"] == "https://new-url"
+        assert result["metadata"]["project_tracking"]["pr_number"] == 200
+        assert result["metadata"]["project_tracking"]["pr_url"] == "https://new-url"
 
 
 class TestUpdateTestCaseWithPrMetadata:
     """Tests for update_test_case_with_pr_metadata function (catalog PRs)."""
 
     def test_adds_catalog_pr_metadata(self) -> None:
-        """Should add all catalog PR metadata fields."""
+        """Should add all catalog PR metadata fields in nested structure."""
         # Create a mock PR object
         mock_pr = MagicMock()
         mock_pr.number = 789
@@ -141,10 +149,10 @@ def test_adds_catalog_pr_metadata(self) -> None:
         test_case: dict[str, Any] = {"title": "Test Case 1"}
         result = update_test_case_with_pr_metadata(test_case, mock_pr, "https://github.com/catalog/repo")
 
-        assert result["catalog_pr_number"] == 789
-        assert result["catalog_pr_url"] == "https://github.com/catalog/repo/pull/789"
-        assert result["catalog_pr_branch"] == "feat/nxos/add-test"
-        assert result["catalog_pr_git_url"] == "https://github.com/catalog/repo"
+        assert result["metadata"]["catalog_tracking"]["pr_number"] == 789
+        assert result["metadata"]["catalog_tracking"]["pr_url"] == "https://github.com/catalog/repo/pull/789"
+        assert result["metadata"]["catalog_tracking"]["pr_branch"] == "feat/nxos/add-test"
+        assert result["metadata"]["catalog_tracking"]["git_url"] == "https://github.com/catalog/repo"
 
 
 class TestRequiresIssueCreation:
@@ -157,20 +165,30 @@ def test_needs_issue_when_no_metadata(self) -> None:
 
     def test_needs_issue_when_only_number(self) -> None:
         """Should return True when only issue number exists."""
-        test_case: dict[str, Any] = {"title": "Test Case 1", "project_issue_number": 123}
+        test_case: dict[str, Any] = {
+            "title": "Test Case 1",
+            "metadata": {"project_tracking": {"issue_number": 123}},
+        }
         assert requires_issue_creation(test_case) is True
 
     def test_needs_issue_when_only_url(self) -> None:
         """Should return True when only issue URL exists."""
-        test_case: dict[str, Any] = {"title": "Test Case 1", "project_issue_url": "https://url"}
+        test_case: dict[str, Any] = {
+            "title": "Test Case 1",
+            "metadata": {"project_tracking": {"issue_url": "https://url"}},
+        }
         assert requires_issue_creation(test_case) is True
 
     def test_no_issue_needed_when_both_exist(self) -> None:
         """Should return False when both issue number and URL exist."""
         test_case: dict[str, Any] = {
             "title": "Test Case 1",
-            "project_issue_number": 123,
-            "project_issue_url": "https://url",
+            "metadata": {
+                "project_tracking": {
+                    "issue_number": 123,
+                    "issue_url": "https://url",
+                }
+            },
         }
         assert requires_issue_creation(test_case) is False
 
@@ -192,11 +210,11 @@ def test_no_pr_needed_when_no_script(self) -> None:
         assert requires_project_pr_creation(test_case) is False
 
     def test_no_pr_needed_when_catalog_destined(self) -> None:
-        """Should return False when catalog_destined is True."""
+        """Should return False when metadata.catalog.destined is True."""
         test_case: dict[str, Any] = {
             "title": "Test Case 1",
             "generated_script_path": "path/to/script.robot",
-            "catalog_destined": True,
+            "metadata": {"catalog": {"destined": True}},
         }
         assert requires_project_pr_creation(test_case) is False
 
@@ -205,8 +223,12 @@ def test_no_pr_needed_when_pr_metadata_exists(self) -> None:
         test_case: dict[str, Any] = {
             "title": "Test Case 1",
             "generated_script_path": "path/to/script.robot",
-            "project_pr_number": 123,
-            "project_pr_url": "https://url",
+            "metadata": {
+                "project_tracking": {
+                    "pr_number": 123,
+                    "pr_url": "https://url",
+                }
+            },
         }
         assert requires_project_pr_creation(test_case) is False
 
@@ -215,7 +237,7 @@ def test_needs_pr_when_only_number_exists(self) -> None:
         test_case: dict[str, Any] = {
             "title": "Test Case 1",
             "generated_script_path": "path/to/script.robot",
-            "project_pr_number": 123,
+            "metadata": {"project_tracking": {"pr_number": 123}},
         }
         assert requires_project_pr_creation(test_case) is True
 
@@ -224,11 +246,11 @@ class TestRequiresCatalogPrCreation:
     """Tests for requires_catalog_pr_creation function."""
 
     def test_needs_catalog_pr_when_catalog_destined(self) -> None:
-        """Should return True when catalog_destined and script exists."""
+        """Should return True when metadata.catalog.destined and script exists."""
         test_case: dict[str, Any] = {
             "title": "Test Case 1",
             "generated_script_path": "path/to/script.robot",
-            "catalog_destined": True,
+            "metadata": {"catalog": {"destined": True}},
         }
         assert requires_catalog_pr_creation(test_case) is True
 
@@ -237,7 +259,7 @@ def test_no_catalog_pr_needed_when_not_catalog_destined(self) -> None:
         test_case: dict[str, Any] = {
             "title": "Test Case 1",
             "generated_script_path": "path/to/script.robot",
-            "catalog_destined": False,
+            "metadata": {"catalog": {"destined": False}},
         }
         assert requires_catalog_pr_creation(test_case) is False
 
@@ -245,7 +267,7 @@ def test_no_catalog_pr_needed_when_no_script(self) -> None:
         """Should return False when no generated script."""
         test_case: dict[str, Any] = {
             "title": "Test Case 1",
-            "catalog_destined": True,
+            "metadata": {"catalog": {"destined": True}},
         }
         assert requires_catalog_pr_creation(test_case) is False
 
@@ -254,9 +276,13 @@ def test_no_catalog_pr_needed_when_metadata_exists(self) -> None:
         test_case: dict[str, Any] = {
             "title": "Test Case 1",
             "generated_script_path": "path/to/script.robot",
-            "catalog_destined": True,
-            "catalog_pr_number": 123,
-            "catalog_pr_url": "https://url",
+            "metadata": {
+                "catalog": {"destined": True},
+                "catalog_tracking": {
+                    "pr_number": 123,
+                    "pr_url": "https://url",
+                },
+            },
         }
         assert requires_catalog_pr_creation(test_case) is False
 
@@ -425,12 +451,11 @@ def test_saves_to_correct_file(self) -> None:
             filepath = tmppath / "my_test_cases.yaml"
             filepath.write_text("test_cases:\n  - title: Test 1\n")
 
-            # Load and modify
+            # Load and modify using nested structure
             test_cases = load_all_test_cases(tmppath)
             if test_cases:  # Only if file was found
                 test_case = test_cases[0]
-                test_case["project_issue_number"] = 999
-                test_case["project_issue_url"] = "https://test-url"
+                update_test_case_with_issue_metadata(test_case, 999, "https://test-url")
 
                 result = save_test_case_metadata(test_case)
 
@@ -438,4 +463,4 @@ def test_saves_to_correct_file(self) -> None:
                 if result:
                     reloaded = load_test_cases_yaml(filepath)
                     assert reloaded is not None
-                    assert reloaded["test_cases"][0]["project_issue_number"] == 999
+                    assert reloaded["test_cases"][0]["metadata"]["project_tracking"]["issue_number"] == 999
diff --git a/tests/unit/test_synchronize_issues_yaml_migration.py b/tests/unit/test_synchronize_issues_yaml_migration.py
index 9105af8..61cc5aa 100644
--- a/tests/unit/test_synchronize_issues_yaml_migration.py
+++ b/tests/unit/test_synchronize_issues_yaml_migration.py
@@ -209,7 +209,7 @@ class TestMigrateIssueFromGithub:
 
     @pytest.mark.asyncio
     async def test_migrates_issue_metadata(self) -> None:
-        """Should migrate issue metadata from GitHub to test case."""
+        """Should migrate issue metadata from GitHub to test case in nested structure."""
         with tempfile.TemporaryDirectory() as tmpdir:
             tmppath = Path(tmpdir)
             test_case_file = tmppath / "my_test_cases.yaml"
@@ -235,12 +235,12 @@ async def test_migrates_issue_metadata(self) -> None:
             )
 
             assert result is True
-            assert test_case["project_issue_number"] == 123
-            assert test_case["project_issue_url"] == "https://github.com/org/repo/issues/123"
+            assert test_case["metadata"]["project_tracking"]["issue_number"] == 123
+            assert test_case["metadata"]["project_tracking"]["issue_url"] == "https://github.com/org/repo/issues/123"
 
     @pytest.mark.asyncio
     async def test_migrates_pr_metadata(self) -> None:
-        """Should migrate PR metadata from GitHub to test case."""
+        """Should migrate PR metadata from GitHub to test case in nested structure."""
         with tempfile.TemporaryDirectory() as tmpdir:
             tmppath = Path(tmpdir)
             test_case_file = tmppath / "my_test_cases.yaml"
@@ -267,9 +267,9 @@ async def test_migrates_pr_metadata(self) -> None:
             )
 
             assert result is True
-            assert test_case["project_pr_number"] == 456
-            assert test_case["project_pr_url"] == "https://github.com/org/repo/pull/456"
-            assert test_case["project_pr_branch"] == "feature/test"
+            assert test_case["metadata"]["project_tracking"]["pr_number"] == 456
+            assert test_case["metadata"]["project_tracking"]["pr_url"] == "https://github.com/org/repo/pull/456"
+            assert test_case["metadata"]["project_tracking"]["pr_branch"] == "feature/test"
 
     @pytest.mark.asyncio
     async def test_returns_false_when_not_found_in_github(self) -> None:
diff --git a/tests/unit/test_synchronize_test_requirements.py b/tests/unit/test_synchronize_test_requirements.py
index 850dcb4..21bd871 100644
--- a/tests/unit/test_synchronize_test_requirements.py
+++ b/tests/unit/test_synchronize_test_requirements.py
@@ -100,7 +100,7 @@ async def test_creates_issue_successfully(self) -> None:
 
     @pytest.mark.asyncio
     async def test_updates_test_case_with_metadata(self) -> None:
-        """Should update test case dict with issue metadata."""
+        """Should update test case dict with issue metadata in nested structure."""
         mock_adapter = AsyncMock()
         mock_issue = MagicMock()
         mock_issue.number = 456
@@ -111,8 +111,8 @@ async def test_updates_test_case_with_metadata(self) -> None:
 
         await create_issue_for_test_case(test_case, mock_adapter, "Body")
 
-        assert test_case["project_issue_number"] == 456
-        assert test_case["project_issue_url"] == "https://github.com/org/repo/issues/456"
+        assert test_case["metadata"]["project_tracking"]["issue_number"] == 456
+        assert test_case["metadata"]["project_tracking"]["issue_url"] == "https://github.com/org/repo/issues/456"
 
     @pytest.mark.asyncio
     async def test_returns_none_on_missing_title(self) -> None:
@@ -195,8 +195,12 @@ async def test_pr_body_includes_issue_reference(self) -> None:
             test_case: dict[str, Any] = {
                 "title": "Test Case 1",
                 "generated_script_path": script_path,
-                "project_issue_number": 42,
-                "project_issue_url": "https://github.com/org/repo/issues/42",
+                "metadata": {
+                    "project_tracking": {
+                        "issue_number": 42,
+                        "issue_url": "https://github.com/org/repo/issues/42",
+                    }
+                },
             }
 
             await create_project_pr_for_test_case(
@@ -477,13 +481,15 @@ async def test_skips_test_cases_with_existing_metadata(self) -> None:
         """Should skip test cases that already have issue metadata."""
         with tempfile.TemporaryDirectory() as tmpdir:
             test_cases_dir = Path(tmpdir)
-            # Create test case file with existing metadata
+            # Create test case file with existing nested metadata
             (test_cases_dir / "my_test_cases.yaml").write_text(
                 """test_cases:
   - title: Test Case 1
     purpose: Test purpose
-    project_issue_number: 123
-    project_issue_url: https://existing-url
+    metadata:
+      project_tracking:
+        issue_number: 123
+        issue_url: https://existing-url
     commands:
       - command: show version
 """
@@ -516,9 +522,11 @@ async def test_creates_project_prs_for_non_catalog(self) -> None:
                 f"""test_cases:
   - title: Test Case 1
     purpose: Test purpose
-    project_issue_number: 1
-    project_issue_url: https://url
     generated_script_path: {script_path}
+    metadata:
+      project_tracking:
+        issue_number: 1
+        issue_url: https://url
     commands:
       - command: show version
 """
@@ -564,10 +572,13 @@ async def test_creates_catalog_prs_for_catalog_destined(self) -> None:
                 f"""test_cases:
   - title: Test Case 1
     purpose: Test purpose
-    project_issue_number: 1
-    project_issue_url: https://url
     generated_script_path: {script_path}
-    catalog_destined: true
+    metadata:
+      project_tracking:
+        issue_number: 1
+        issue_url: https://url
+      catalog:
+        destined: true
     commands:
       - command: show version
 """
@@ -619,10 +630,13 @@ async def test_reports_error_when_catalog_not_configured(self) -> None:
                 f"""test_cases:
   - title: Test Case 1
     purpose: Test purpose
-    project_issue_number: 1
-    project_issue_url: https://url
     generated_script_path: {script_path}
-    catalog_destined: true
+    metadata:
+      project_tracking:
+        issue_number: 1
+        issue_url: https://url
+      catalog:
+        destined: true
     commands:
       - command: show version
 """