diff --git a/Sources/SubtreeLib/Utilities/GitOperations.swift b/Sources/SubtreeLib/Utilities/GitOperations.swift
index 01b384b..e0497e1 100644
--- a/Sources/SubtreeLib/Utilities/GitOperations.swift
+++ b/Sources/SubtreeLib/Utilities/GitOperations.swift
@@ -125,8 +125,107 @@ public enum GitOperations {
         return (stdout, stderr, exitCode)
     }
     
+    /// Information about a subtree's split tracking state
+    public struct SubtreeSplitInfo: Sendable {
+        /// The split hash recorded for this prefix
+        public let splitHash: String
+        /// Whether the commit containing this trailer also has trailers for other prefixes
+        public let isMultiTrailer: Bool
+        /// The commit hash where the trailer was found
+        public let commitHash: String
+    }
+    
+    /// Find the most recent subtree split info for a given prefix
+    ///
+    /// Scans git log for commits containing `git-subtree-dir: <prefix>` and extracts
+    /// the corresponding `git-subtree-split` hash. Also detects if the commit has
+    /// trailers for multiple different prefixes (multi-trailer merge commits).
+    ///
+    /// - Parameter prefix: The subtree prefix directory (e.g., "Vendor/secp256k1")
+    /// - Returns: Split info if found, nil if no subtree tracking exists for this prefix
+    /// - Throws: GitError if git commands fail
+    public static func findSubtreeSplitInfo(prefix: String) async throws -> SubtreeSplitInfo? {
+        // Find the most recent commit with a git-subtree-dir trailer matching this prefix
+        let logResult = try await run(arguments: [
+            "log", "--all", "--grep=^git-subtree-dir: \(prefix)$",
+            "--format=%H%n%B", "-1"
+        ])
+        
+        guard logResult.exitCode == 0, !logResult.stdout.trimmingCharacters(in: .whitespacesAndNewlines).isEmpty else {
+            return nil
+        }
+        
+        let output = logResult.stdout
+        let lines = output.components(separatedBy: "\n")
+        guard let commitHash = lines.first, !commitHash.isEmpty else {
+            return nil
+        }
+        
+        // Parse all git-subtree-dir and git-subtree-split pairs from the commit message
+        var dirSplitPairs: [(dir: String, split: String)] = []
+        var currentDir: String?
+        
+        for line in lines.dropFirst() {
+            let trimmed = line.trimmingCharacters(in: .whitespaces)
+            if trimmed.hasPrefix("git-subtree-dir: ") {
+                currentDir = String(trimmed.dropFirst("git-subtree-dir: ".count))
+            } else if trimmed.hasPrefix("git-subtree-split: "), let dir = currentDir {
+                let split = String(trimmed.dropFirst("git-subtree-split: ".count))
+                dirSplitPairs.append((dir: dir, split: split))
+                currentDir = nil
+            }
+        }
+        
+        // Find the split hash for our target prefix
+        guard let matchingPair = dirSplitPairs.first(where: { $0.dir == prefix }) else {
+            return nil
+        }
+        
+        // Count unique prefixes to detect multi-trailer commits
+        let uniquePrefixes = Set(dirSplitPairs.map { $0.dir })
+        
+        return SubtreeSplitInfo(
+            splitHash: matchingPair.split,
+            isMultiTrailer: uniquePrefixes.count > 1,
+            commitHash: commitHash
+        )
+    }
+    
+    /// Create a resync commit to fix multi-trailer split tracking
+    ///
+    /// When a merge commit contains `git-subtree-dir`/`git-subtree-split` trailers for
+    /// multiple different prefixes, `git subtree pull` can pick the wrong split hash.
+    /// This creates an empty commit with a single correct trailer so `git subtree`
+    /// finds it first (newest) and uses the right split hash.
+    ///
+    /// - Parameters:
+    ///   - prefix: The subtree prefix directory
+    ///   - splitHash: The correct split hash for this prefix
+    /// - Throws: GitError if the commit fails
+    public static func createResyncCommit(prefix: String, splitHash: String) async throws {
+        let shortHash = String(splitHash.prefix(8))
+        let message = """
+        Squashed '\(prefix)/' content from commit \(shortHash)
+        
+        git-subtree-dir: \(prefix)
+        git-subtree-split: \(splitHash)
+        """
+        
+        let result = try await run(arguments: [
+            "commit", "--allow-empty", "-m", message
+        ])
+        guard result.exitCode == 0 else {
+            throw GitError.commandFailed("Failed to create resync commit: \(result.stderr)")
+        }
+    }
+    
     // T006: Git subtree pull wrapper for update operations
     /// Execute git subtree pull to update a subtree
+    ///
+    /// Before pulling, checks for multi-trailer merge commits that can confuse
+    /// `git subtree`'s split hash detection. If found, creates a resync commit
+    /// with the correct single-prefix trailer to fix the issue transparently.
+    ///
     /// - Parameters:
     ///   - prefix: Local directory path for the subtree
     ///   - remote: Git remote URL
@@ -135,6 +234,13 @@ public enum GitOperations {
     /// - Returns: Commit hash of the pulled changes
     /// - Throws: GitError if operation fails
     public static func subtreePull(prefix: String, remote: String, ref: String, squash: Bool) async throws -> String {
+        // Pre-flight: detect and fix multi-trailer split tracking
+        if squash, let splitInfo = try? await findSubtreeSplitInfo(prefix: prefix) {
+            if splitInfo.isMultiTrailer {
+                try await createResyncCommit(prefix: prefix, splitHash: splitInfo.splitHash)
+            }
+        }
+        
         var args = ["subtree", "pull", "--prefix=\(prefix)"]
         if squash {
             args.append("--squash")
diff --git a/Tests/IntegrationTests/MultiTrailerResyncTests.swift b/Tests/IntegrationTests/MultiTrailerResyncTests.swift
new file mode 100644
index 0000000..27776e8
--- /dev/null
+++ b/Tests/IntegrationTests/MultiTrailerResyncTests.swift
@@ -0,0 +1,203 @@
+import Testing
+import Foundation
+#if canImport(System)
+import System
+#else
+import SystemPackage
+#endif
+
+@Suite("Multi-Trailer Resync Tests")
+final class MultiTrailerResyncTests {
+    
+    let harness = TestHarness()
+    
+    /// Helper: get the file:// URL for a fixture's path
+    private func fileURL(for fixture: GitRepositoryFixture) -> String {
+        "file://\(fixture.path.string)"
+    }
+    
+    /// Helper: create a bare upstream repo with an initial commit and tag
+    private func createUpstreamRepo(name: String, tag: String) async throws -> GitRepositoryFixture {
+        let upstream = try await GitRepositoryFixture()
+        
+        // Add a source file so the subtree has content
+        let srcDir = upstream.path.appending("src")
+        try FileManager.default.createDirectory(atPath: srcDir.string, withIntermediateDirectories: true)
+        try "int main() { return 0; }\n".write(
+            toFile: srcDir.appending("main.c").string, atomically: true, encoding: .utf8
+        )
+        try await upstream.runGit(["add", "."])
+        try await upstream.runGit(["commit", "-m", "Add source files"])
+        try await upstream.runGit(["tag", tag])
+        
+        return upstream
+    }
+    
+    /// Helper: add new content to upstream and tag it
+    private func addUpstreamUpdate(repo: GitRepositoryFixture, tag: String) async throws {
+        try "// updated\n".write(
+            toFile: repo.path.appending("src/main.c").string, atomically: true, encoding: .utf8
+        )
+        try await repo.runGit(["add", "."])
+        try await repo.runGit(["commit", "-m", "Update for \(tag)"])
+        try await repo.runGit(["tag", tag])
+    }
+    
+    /// Helper: get the full commit hash for a tag in a repo
+    private func getTagCommit(repo: GitRepositoryFixture, tag: String) async throws -> String {
+        let output = try await repo.runGit(["rev-parse", tag])
+        return output.trimmingCharacters(in: .whitespacesAndNewlines)
+    }
+    
+    // MARK: - Multi-Trailer Detection Tests
+    
+    @Test("update succeeds when multi-trailer merge commit exists")
+    func testUpdateWithMultiTrailerCommit() async throws {
+        // Create two upstream repos
+        let upstreamA = try await createUpstreamRepo(name: "libA", tag: "v1.0")
+        defer { try? upstreamA.tearDown() }
+        let upstreamB = try await createUpstreamRepo(name: "libB", tag: "v1.0")
+        defer { try? upstreamB.tearDown() }
+        
+        // Create consumer repo
+        let local = try await GitRepositoryFixture()
+        defer { try? local.tearDown() }
+        
+        // Init subtree config
+        _ = try await harness.run(arguments: ["init"], workingDirectory: local.path)
+        
+        // Add both subtrees individually
+        let addA = try await harness.run(
+            arguments: ["add", "--remote", fileURL(for: upstreamA), "--name", "libA",
+                        "--prefix", "Vendor/libA", "--ref", "v1.0"],
+            workingDirectory: local.path
+        )
+        #expect(addA.exitCode == 0, "Add libA should succeed: \(addA.stderr)")
+        
+        let addB = try await harness.run(
+            arguments: ["add", "--remote", fileURL(for: upstreamB), "--name", "libB",
+                        "--prefix", "Vendor/libB", "--ref", "v1.0"],
+            workingDirectory: local.path
+        )
+        #expect(addB.exitCode == 0, "Add libB should succeed: \(addB.stderr)")
+        
+        // Get the split hashes from the individual subtree add commits
+        let commitHashA = try await getTagCommit(repo: upstreamA, tag: "v1.0")
+        let commitHashB = try await getTagCommit(repo: upstreamB, tag: "v1.0")
+        
+        // Create a multi-trailer commit (simulates squash-merged PR that combined both adds)
+        let multiTrailerMessage = """
+        refactor: Replace submodules with subtrees
+        
+        git-subtree-dir: Vendor/libA
+        git-subtree-split: \(commitHashA)
+        git-subtree-dir: Vendor/libB
+        git-subtree-split: \(commitHashB)
+        """
+        try await local.runGit(["commit", "--allow-empty", "-m", multiTrailerMessage])
+        
+        // Add new content to upstream A and tag v2.0
+        try await addUpstreamUpdate(repo: upstreamA, tag: "v2.0")
+        
+        // Update libA — this should trigger resync and succeed
+        let updateResult = try await harness.run(
+            arguments: ["update", "libA"],
+            workingDirectory: local.path
+        )
+        
+        #expect(updateResult.exitCode == 0,
+                "Update should succeed after multi-trailer resync: \(updateResult.stdout)\(updateResult.stderr)")
+        #expect(updateResult.stdout.contains("Updated libA") || updateResult.stdout.contains("up to date"),
+                "Should show update status")
+    }
+    
+    @Test("update succeeds when no multi-trailer issue exists")
+    func testUpdateWithoutMultiTrailerCommit() async throws {
+        // Create upstream repo
+        let upstream = try await createUpstreamRepo(name: "lib", tag: "v1.0")
+        defer { try? upstream.tearDown() }
+        
+        // Create consumer repo
+        let local = try await GitRepositoryFixture()
+        defer { try? local.tearDown() }
+        
+        // Init and add subtree
+        _ = try await harness.run(arguments: ["init"], workingDirectory: local.path)
+        let addResult = try await harness.run(
+            arguments: ["add", "--remote", fileURL(for: upstream), "--name", "lib",
+                        "--prefix", "Vendor/lib", "--ref", "v1.0"],
+            workingDirectory: local.path
+        )
+        #expect(addResult.exitCode == 0, "Add should succeed")
+        
+        // Add new content upstream
+        try await addUpstreamUpdate(repo: upstream, tag: "v2.0")
+        
+        // Update should succeed normally (no multi-trailer issue)
+        let updateResult = try await harness.run(
+            arguments: ["update", "lib"],
+            workingDirectory: local.path
+        )
+        
+        #expect(updateResult.exitCode == 0, "Update should succeed: \(updateResult.stdout)\(updateResult.stderr)")
+        #expect(updateResult.stdout.contains("Updated lib"), "Should show updated message")
+    }
+    
+    @Test("resync commit has correct single-prefix trailer")
+    func testResyncCommitFormat() async throws {
+        // Create two upstream repos
+        let upstreamA = try await createUpstreamRepo(name: "libA", tag: "v1.0")
+        defer { try? upstreamA.tearDown() }
+        let upstreamB = try await createUpstreamRepo(name: "libB", tag: "v1.0")
+        defer { try? upstreamB.tearDown() }
+        
+        // Create consumer repo
+        let local = try await GitRepositoryFixture()
+        defer { try? local.tearDown() }
+        
+        // Init and add both subtrees
+        _ = try await harness.run(arguments: ["init"], workingDirectory: local.path)
+        _ = try await harness.run(
+            arguments: ["add", "--remote", fileURL(for: upstreamA), "--name", "libA",
+                        "--prefix", "Vendor/libA", "--ref", "v1.0"],
+            workingDirectory: local.path
+        )
+        _ = try await harness.run(
+            arguments: ["add", "--remote", fileURL(for: upstreamB), "--name", "libB",
+                        "--prefix", "Vendor/libB", "--ref", "v1.0"],
+            workingDirectory: local.path
+        )
+        
+        // Create multi-trailer commit
+        let commitHashA = try await getTagCommit(repo: upstreamA, tag: "v1.0")
+        let commitHashB = try await getTagCommit(repo: upstreamB, tag: "v1.0")
+        let multiTrailerMessage = """
+        combined subtree adds
+        
+        git-subtree-dir: Vendor/libA
+        git-subtree-split: \(commitHashA)
+        git-subtree-dir: Vendor/libB
+        git-subtree-split: \(commitHashB)
+        """
+        try await local.runGit(["commit", "--allow-empty", "-m", multiTrailerMessage])
+        
+        let commitsBefore = try await local.getCommitCount()
+        
+        // Add upstream update and run update
+        try await addUpstreamUpdate(repo: upstreamA, tag: "v2.0")
+        let updateResult = try await harness.run(
+            arguments: ["update", "libA"],
+            workingDirectory: local.path
+        )
+        #expect(updateResult.exitCode == 0, "Update should succeed")
+        
+        // Verify a resync commit was created (commit count should be higher than expected)
+        // Expected: +1 resync + 1 subtree pull merge + amend = at least commitsBefore + 2
+        let commitsAfter = try await local.getCommitCount()
+        #expect(commitsAfter > commitsBefore, "Should have new commits from resync + update")
+        
+        // Verify the resync commit exists with correct format
+        let log = try await local.runGit(["log", "--all", "--oneline", "--grep=git-subtree-dir: Vendor/libA"])
+        #expect(log.contains("Squashed 'Vendor/libA/'"), "Should contain resync commit")
+    }
+}