diff --git a/apps/backend/internal/worktree/manager_git.go b/apps/backend/internal/worktree/manager_git.go
index 02eb6f68b2..7892bb486d 100644
--- a/apps/backend/internal/worktree/manager_git.go
+++ b/apps/backend/internal/worktree/manager_git.go
@@ -168,12 +168,6 @@ func (m *Manager) BranchRecoveryStatus(ctx context.Context, repoPath, branch str
 // wait, timeout, missing ref) returns false, and callers must treat that as
 // "cannot rule out loss": being slightly stale is recoverable, silently
 // dropping the user's unpushed commits is not.
-//
-// NOTE: PR #2654 adds an equivalent `isAncestor` helper on the
-// pullCurrentBranchOrFallback path, with the arguments in the opposite order.
-// The two are deliberately named differently so both can land in either order
-// without a duplicate-symbol build failure; whichever merges second should
-// collapse them into one helper.
 func (m *Manager) refContains(ctx context.Context, repoPath, container, contained string) bool {
 	// Same Acquire-then-build-execCtx ordering as branchExists.
 	release, err := subproc.AcquireGit(ctx, subproc.GitLifecycle)
@@ -338,14 +332,27 @@ func (m *Manager) pullCurrentBranchOrFallback(
 	output, err, execCtxErr := m.runGitCombinedAfterAcquire(ctx, m.pullTimeout, repoPath, "pull", "--ff-only", "origin", baseBranch)
 	if err != nil {
 		reason := classifyGitFallbackReason(err, string(output), execCtxErr)
-		m.logger.Warn("git pull failed before worktree creation; continuing with remote ref",
+		// The preceding fetch succeeded, so origin/<branch> holds the latest
+		// remote state and is normally the better start point. It is only
+		// better when it is *ahead* of the local branch, though: if the local
+		// branch carries commits origin does not have, starting from the
+		// remote ref silently drops them from the new worktree, and creation
+		// still succeeds so nothing surfaces the loss. Keep the local branch
+		// in that case, matching handleFetchFallback and the non-current-branch
+		// path in resolveLocalBaseRef, which both resolve to it on failure.
+		fallbackRef := remoteRef
+		if !m.refContains(ctx, repoPath, remoteRef, baseBranch) {
+			fallbackRef = baseBranch
+		}
+		m.logger.Warn("git pull failed before worktree creation; continuing with fallback ref",
 			zap.String("branch", baseBranch),
 			zap.String("reason", reason),
 			zap.String("remote_ref", remoteRef),
+			zap.String("fallback_ref", fallbackRef),
 			zap.String("output", string(output)),
 			zap.Error(err))
-		m.reportSyncCompleted(stepName, onProgress, fmt.Sprintf("Pull %s; using %s", reason, remoteRef), string(output))
-		return remoteRef
+		m.reportSyncCompleted(stepName, onProgress, fmt.Sprintf("Pull %s; using %s", reason, fallbackRef), string(output))
+		return fallbackRef
 	}
 	m.reportSyncCompleted(stepName, onProgress, fmt.Sprintf("Synced and using %s", baseBranch), "")
 	return baseBranch
diff --git a/apps/backend/internal/worktree/manager_pull_fallback_test.go b/apps/backend/internal/worktree/manager_pull_fallback_test.go
new file mode 100644
index 0000000000..2eef5dec43
--- /dev/null
+++ b/apps/backend/internal/worktree/manager_pull_fallback_test.go
@@ -0,0 +1,163 @@
+package worktree
+
+import (
+	"context"
+	"path/filepath"
+	"strings"
+	"testing"
+)
+
+// initGitRepoWithOriginAheadLocal builds the shape that matters here: a normal
+// repository sitting on `main`, wired to a reachable bare `origin`, whose local
+// `main` carries a commit that was never pushed. origin/main is therefore a
+// strict ancestor of local main.
+//
+// Returns the working repository path and the local-only commit SHA.
+func initGitRepoWithOriginAheadLocal(t *testing.T) (string, string) {
+	t.Helper()
+
+	base := t.TempDir()
+	originPath := filepath.Join(base, "origin.git")
+	repoPath := filepath.Join(base, "repo")
+
+	runGit(t, base, "init", "--bare", "-b", "main", originPath)
+	runGit(t, base, "init", "-b", "main", repoPath)
+	runGit(t, repoPath, "config", "user.email", "test@example.com")
+	runGit(t, repoPath, "config", "user.name", "Test User")
+	runGit(t, repoPath, "config", "commit.gpgsign", "false")
+
+	writeRepoFile(t, repoPath, "README.md", "initial\n")
+	runGit(t, repoPath, "add", "README.md")
+	runGit(t, repoPath, "commit", "-m", "initial commit")
+	runGit(t, repoPath, "remote", "add", "origin", originPath)
+	runGit(t, repoPath, "push", "origin", "main")
+
+	// The commit that only exists locally — the equivalent of a user's unpushed
+	// work on their base branch.
+	writeRepoFile(t, repoPath, "local-only.txt", "unpushed\n")
+	runGit(t, repoPath, "add", "local-only.txt")
+	runGit(t, repoPath, "commit", "-m", "local-only commit")
+
+	localHead := strings.TrimSpace(runGit(t, repoPath, "rev-parse", "main"))
+	return repoPath, localHead
+}
+
+// captureSyncProgress records every SyncProgressEvent so a test can assert
+// which branch of the sync actually ran, not merely what it returned.
+func captureSyncProgress(events *[]SyncProgressEvent) SyncProgressCallback {
+	return func(event SyncProgressEvent) { *events = append(*events, event) }
+}
+
+// syncOutputs joins the captured progress output for assertion messages.
+func syncOutputs(events []SyncProgressEvent) string {
+	parts := make([]string, 0, len(events))
+	for _, e := range events {
+		parts = append(parts, e.Output)
+	}
+	return strings.Join(parts, " | ")
+}
+
+// TestPullBaseBranch_PullFailureKeepsLocalCommits pins the behaviour that a
+// transient `git pull` failure must not silently rebase the worktree's starting
+// point onto origin/<branch>.
+//
+// When the pull fails for an environmental reason (throttle contention, a
+// timeout, a stale index.lock) origin/<branch> is not fresher than the local
+// branch — here it is a strict ancestor of it. Returning the remote ref
+// therefore discards the user's unpushed commits from the new worktree, and it
+// does so silently: creation still succeeds, so nothing surfaces the loss.
+//
+// The two sibling fallbacks in manager_git.go (handleFetchFallback, and the
+// non-current-branch path in resolveLocalBaseRef) already resolve to the local
+// branch on failure. This one must agree with them.
+func TestPullBaseBranch_PullFailureKeepsLocalCommits(t *testing.T) {
+	repoPath, localHead := initGitRepoWithOriginAheadLocal(t)
+
+	mgr, err := NewManager(newTestConfig(t), newMockStore(), newTestLogger())
+	if err != nil {
+		t.Fatalf("NewManager failed: %v", err)
+	}
+	// Let the fetch succeed (so we reach the pull) but force the pull to fail
+	// the way contention makes it fail in a loaded run. A zero timeout yields
+	// an already-expired context, so the pull cannot accidentally succeed.
+	mgr.pullTimeout = 0
+
+	var events []SyncProgressEvent
+	resolved := mgr.pullBaseBranch(context.Background(), repoPath, "main", captureSyncProgress(&events))
+	if resolved == "" {
+		t.Fatal("pullBaseBranch returned an empty ref")
+	}
+
+	// Prove the failure path actually ran. Both the success and failure paths
+	// resolve to `main` here, so the SHA assertion below cannot distinguish
+	// them on its own — without this the test would pass vacuously if the pull
+	// ever succeeded. The failure path reports "Pull <reason>; using <ref>",
+	// the success path "Synced and using <ref>".
+	outputs := syncOutputs(events)
+	if !strings.Contains(outputs, "Pull ") {
+		t.Fatalf(
+			"pull was expected to fail and take the fallback path, but sync progress was %q;\n"+
+				"the assertion below would pass without exercising the fallback",
+			outputs,
+		)
+	}
+
+	// Assert on the commit the ref actually points at, not on the ref's name:
+	// the defect is that the worktree starts from the wrong commit, and a
+	// name-only assertion would still pass if the mapping changed.
+	resolvedSHA := strings.TrimSpace(runGit(t, repoPath, "rev-parse", resolved))
+	if resolvedSHA != localHead {
+		t.Fatalf(
+			"pullBaseBranch resolved %q to %s, which drops the unpushed local commit %s;\n"+
+				"a failed pull must not move the worktree base backwards onto origin/main",
+			resolved, resolvedSHA, localHead,
+		)
+	}
+}
+
+// TestPullBaseBranch_SuccessfulPullStillAdoptsRemoteCommits guards the happy
+// path the fix must not regress: when the pull succeeds, the base branch is
+// fast-forwarded and the worktree starts from the updated local branch, which
+// now contains the remote commit.
+func TestPullBaseBranch_SuccessfulPullStillAdoptsRemoteCommits(t *testing.T) {
+	base := t.TempDir()
+	originPath := filepath.Join(base, "origin.git")
+	repoPath := filepath.Join(base, "repo")
+	otherPath := filepath.Join(base, "other")
+
+	runGit(t, base, "init", "--bare", "-b", "main", originPath)
+	runGit(t, base, "init", "-b", "main", repoPath)
+	runGit(t, repoPath, "config", "user.email", "test@example.com")
+	runGit(t, repoPath, "config", "user.name", "Test User")
+	runGit(t, repoPath, "config", "commit.gpgsign", "false")
+	writeRepoFile(t, repoPath, "README.md", "initial\n")
+	runGit(t, repoPath, "add", "README.md")
+	runGit(t, repoPath, "commit", "-m", "initial commit")
+	runGit(t, repoPath, "remote", "add", "origin", originPath)
+	runGit(t, repoPath, "push", "origin", "main")
+
+	// A second clone pushes a commit the working repo has not seen yet.
+	runGit(t, base, "clone", originPath, otherPath)
+	runGit(t, otherPath, "config", "user.email", "other@example.com")
+	runGit(t, otherPath, "config", "user.name", "Other User")
+	runGit(t, otherPath, "config", "commit.gpgsign", "false")
+	writeRepoFile(t, otherPath, "remote-only.txt", "pushed\n")
+	runGit(t, otherPath, "add", "remote-only.txt")
+	runGit(t, otherPath, "commit", "-m", "remote-only commit")
+	runGit(t, otherPath, "push", "origin", "main")
+	remoteHead := strings.TrimSpace(runGit(t, otherPath, "rev-parse", "HEAD"))
+
+	mgr, err := NewManager(newTestConfig(t), newMockStore(), newTestLogger())
+	if err != nil {
+		t.Fatalf("NewManager failed: %v", err)
+	}
+
+	resolved := mgr.pullBaseBranch(context.Background(), repoPath, "main", nil)
+	resolvedSHA := strings.TrimSpace(runGit(t, repoPath, "rev-parse", resolved))
+	if resolvedSHA != remoteHead {
+		t.Fatalf(
+			"pullBaseBranch resolved %q to %s, want the pulled remote commit %s",
+			resolved, resolvedSHA, remoteHead,
+		)
+	}
+}