diff --git a/src/resources/extensions/gsd/auto.ts b/src/resources/extensions/gsd/auto.ts
index e01c29147..c807a878d 100644
--- a/src/resources/extensions/gsd/auto.ts
+++ b/src/resources/extensions/gsd/auto.ts
@@ -590,8 +590,11 @@ export async function stopAuto(
     // When the milestone is complete (has a SUMMARY), merge the worktree branch
     // back to main so code isn't stranded on the worktree branch (#2317).
     // For incomplete milestones, preserve the branch for later resumption.
+    //
+    // Skip if phases.ts already merged this milestone — avoids the double
+    // mergeAndExit that fails because the branch was already deleted (#2645).
     try {
-      if (s.currentMilestoneId) {
+      if (s.currentMilestoneId && !s.milestoneMergedInPhases) {
         const notifyCtx = ctx
           ? { notify: ctx.ui.notify.bind(ctx.ui) }
           : { notify: () => {} };
diff --git a/src/resources/extensions/gsd/auto/phases.ts b/src/resources/extensions/gsd/auto/phases.ts
index 0f0976752..040d038c0 100644
--- a/src/resources/extensions/gsd/auto/phases.ts
+++ b/src/resources/extensions/gsd/auto/phases.ts
@@ -333,6 +333,8 @@ export async function runPreDispatch(
       if (s.currentMilestoneId) {
         try {
           deps.resolver.mergeAndExit(s.currentMilestoneId, ctx.ui);
+          // Prevent stopAuto from attempting the same merge (#2645)
+          s.milestoneMergedInPhases = true;
         } catch (mergeErr) {
           if (mergeErr instanceof MergeConflictError) {
             ctx.ui.notify(
@@ -428,6 +430,8 @@ export async function runPreDispatch(
     if (s.currentMilestoneId) {
       try {
         deps.resolver.mergeAndExit(s.currentMilestoneId, ctx.ui);
+        // Prevent stopAuto from attempting the same merge (#2645)
+        s.milestoneMergedInPhases = true;
       } catch (mergeErr) {
         if (mergeErr instanceof MergeConflictError) {
           ctx.ui.notify(
diff --git a/src/resources/extensions/gsd/auto/session.ts b/src/resources/extensions/gsd/auto/session.ts
index 035b3c6ab..9ca66a963 100644
--- a/src/resources/extensions/gsd/auto/session.ts
+++ b/src/resources/extensions/gsd/auto/session.ts
@@ -122,6 +122,11 @@ export class AutoSession {
   /** Set to true when worktree creation fails; prevents merge of nonexistent branch. */
   isolationDegraded = false;
 
+  // ── Merge guard ──────────────────────────────────────────────────────
+  /** Set to true after phases.ts successfully calls mergeAndExit, so that
+   *  stopAuto does not attempt the same merge a second time (#2645). */
+  milestoneMergedInPhases = false;
+
   // ── Dispatch circuit breakers ──────────────────────────────────────
   rewriteAttemptCount = 0;
 
@@ -205,6 +210,7 @@ export class AutoSession {
     this.sidecarQueue = [];
     this.rewriteAttemptCount = 0;
     this.isolationDegraded = false;
+    this.milestoneMergedInPhases = false;
 
     // Signal handler
     this.sigtermHandler = null;
diff --git a/src/resources/extensions/gsd/tests/double-merge-guard.test.ts b/src/resources/extensions/gsd/tests/double-merge-guard.test.ts
new file mode 100644
index 000000000..ccc9385fc
--- /dev/null
+++ b/src/resources/extensions/gsd/tests/double-merge-guard.test.ts
@@ -0,0 +1,97 @@
+import { describe, test } from "node:test";
+import assert from "node:assert/strict";
+import { readFileSync } from "node:fs";
+import { join, dirname } from "node:path";
+import { fileURLToPath } from "node:url";
+import { AutoSession } from "../auto/session.ts";
+
+const __dirname = dirname(fileURLToPath(import.meta.url));
+
+describe("double mergeAndExit guard (#2645)", () => {
+  test("phases.ts sets milestoneMergedInPhases after mergeAndExit in milestone-complete path", () => {
+    // Source audit: the "complete" phase path must set the guard flag
+    // after calling mergeAndExit so that stopAuto skips the second merge.
+    const phasesSrc = readFileSync(
+      join(__dirname, "..", "auto", "phases.ts"),
+      "utf-8",
+    );
+
+    // Find the "complete" phase block
+    const completeIdx = phasesSrc.indexOf('state.phase === "complete"');
+    assert.ok(completeIdx > 0, "phases.ts should have a 'complete' phase check");
+
+    const afterComplete = phasesSrc.slice(completeIdx, completeIdx + 600);
+    const mergeIdx = afterComplete.indexOf("deps.resolver.mergeAndExit");
+    const flagIdx = afterComplete.indexOf("s.milestoneMergedInPhases = true");
+
+    assert.ok(mergeIdx > 0, "complete path should call mergeAndExit");
+    assert.ok(flagIdx > 0, "complete path should set milestoneMergedInPhases");
+    assert.ok(
+      flagIdx > mergeIdx,
+      "milestoneMergedInPhases must be set AFTER mergeAndExit (not before)",
+    );
+  });
+
+  test("phases.ts sets milestoneMergedInPhases after mergeAndExit in all-milestones-complete path", () => {
+    const phasesSrc = readFileSync(
+      join(__dirname, "..", "auto", "phases.ts"),
+      "utf-8",
+    );
+
+    // The "all milestones complete" block checks incomplete.length === 0
+    const allCompleteIdx = phasesSrc.indexOf("incomplete.length === 0");
+    assert.ok(allCompleteIdx > 0, "phases.ts should have an all-milestones-complete check");
+
+    const afterAllComplete = phasesSrc.slice(allCompleteIdx, allCompleteIdx + 600);
+    const mergeIdx = afterAllComplete.indexOf("deps.resolver.mergeAndExit");
+    const flagIdx = afterAllComplete.indexOf("s.milestoneMergedInPhases = true");
+
+    assert.ok(mergeIdx > 0, "all-complete path should call mergeAndExit");
+    assert.ok(flagIdx > 0, "all-complete path should set milestoneMergedInPhases");
+    assert.ok(
+      flagIdx > mergeIdx,
+      "milestoneMergedInPhases must be set AFTER mergeAndExit (not before)",
+    );
+  });
+
+  test("stopAuto checks milestoneMergedInPhases before calling mergeAndExit", () => {
+    const autoSrc = readFileSync(
+      join(__dirname, "..", "auto.ts"),
+      "utf-8",
+    );
+
+    // The Step 4 worktree exit block must check the guard flag
+    const step4Idx = autoSrc.indexOf("Step 4: Auto-worktree exit");
+    assert.ok(step4Idx > 0, "auto.ts should have Step 4 worktree exit");
+
+    const step4Block = autoSrc.slice(step4Idx, step4Idx + 600);
+    assert.ok(
+      step4Block.includes("milestoneMergedInPhases"),
+      "stopAuto Step 4 must check milestoneMergedInPhases before merging",
+    );
+    assert.ok(
+      step4Block.includes("!s.milestoneMergedInPhases"),
+      "stopAuto should skip merge when milestoneMergedInPhases is true",
+    );
+  });
+
+  test("AutoSession.milestoneMergedInPhases defaults to false", () => {
+    const session = new AutoSession();
+    assert.equal(
+      session.milestoneMergedInPhases,
+      false,
+      "new session should have milestoneMergedInPhases = false",
+    );
+  });
+
+  test("AutoSession.reset() clears milestoneMergedInPhases", () => {
+    const session = new AutoSession();
+    session.milestoneMergedInPhases = true;
+    session.reset();
+    assert.equal(
+      session.milestoneMergedInPhases,
+      false,
+      "reset() should clear milestoneMergedInPhases back to false",
+    );
+  });
+});