diff --git a/src/resources/extensions/gsd/auto-worktree.ts b/src/resources/extensions/gsd/auto-worktree.ts
index eb7435b6a..0ff06f4bf 100644
--- a/src/resources/extensions/gsd/auto-worktree.ts
+++ b/src/resources/extensions/gsd/auto-worktree.ts
@@ -1057,12 +1057,20 @@ export function createAutoWorktree(
       reuseExistingBranch: true,
     });
   } else {
-    // Fresh start — create branch from integration branch
+    // Fresh start — create branch from integration branch.
+    // Use the same 3-tier fallback as mergeMilestoneToMain (#3461):
+    //   1. META.json integration branch (explicit per-milestone override)
+    //   2. git.main_branch preference (user's configured working branch)
+    //   3. nativeDetectMainBranch (origin/HEAD auto-detection)
+    // Without tier 2, projects with main_branch=dev but origin/HEAD→master
+    // would fork worktrees from the wrong (stale) branch.
     const integrationBranch =
       readIntegrationBranch(basePath, milestoneId) ?? undefined;
+    const gitPrefs = loadEffectiveGSDPreferences()?.preferences?.git;
+    const startPoint = integrationBranch ?? gitPrefs?.main_branch ?? undefined;
     info = createWorktree(basePath, milestoneId, {
       branch,
-      startPoint: integrationBranch,
+      startPoint,
     });
   }
 
diff --git a/src/resources/extensions/gsd/tests/worktree-main-branch.test.ts b/src/resources/extensions/gsd/tests/worktree-main-branch.test.ts
new file mode 100644
index 000000000..f691f73bd
--- /dev/null
+++ b/src/resources/extensions/gsd/tests/worktree-main-branch.test.ts
@@ -0,0 +1,20 @@
+/**
+ * Regression test for #3461: createAutoWorktree must use git.main_branch
+ * preference when META.json integration branch is absent.
+ */
+import { test } from "node:test";
+import assert from "node:assert/strict";
+import { readFileSync } from "node:fs";
+import { join } from "node:path";
+
+test("auto-worktree.ts includes main_branch preference in startPoint fallback (#3461)", () => {
+  const src = readFileSync(
+    join(import.meta.dirname, "..", "auto-worktree.ts"),
+    "utf-8",
+  );
+  // The fix adds gitPrefs?.main_branch to the startPoint fallback chain
+  assert.ok(
+    src.includes("gitPrefs?.main_branch") || src.includes("prefs.main_branch"),
+    "createAutoWorktree must check git.main_branch preference before falling back to nativeDetectMainBranch",
+  );
+});