diff --git a/src/resources/extensions/gsd/auto-timers.ts b/src/resources/extensions/gsd/auto-timers.ts
index 2b14365d0..b2faa0c44 100644
--- a/src/resources/extensions/gsd/auto-timers.ts
+++ b/src/resources/extensions/gsd/auto-timers.ts
@@ -122,6 +122,10 @@ export function startUnitSupervision(sctx: SupervisionContext): void {
       phase: "wrapup-warning-sent",
       wrapupWarningSent: true,
     });
+    // Only trigger a new turn if no tools are currently in flight.
+    // Triggering during active tool calls causes tool results to be skipped
+    // with "Skipped due to queued user message", leading to provider errors (#3512).
+    const softTrigger = getInFlightToolCount() === 0;
     pi.sendMessage(
       {
         customType: "gsd-auto-wrapup",
@@ -136,7 +140,7 @@ export function startUnitSupervision(sctx: SupervisionContext): void {
           "4. leave precise resume notes if anything remains unfinished",
         ].join("\n"),
       },
-      { triggerTurn: true },
+      { triggerTurn: softTrigger },
     );
   }, softTimeoutMs);
 
@@ -293,6 +297,8 @@ export function startUnitSupervision(sctx: SupervisionContext): void {
       );
     }
 
+    // Only trigger a new turn if no tools are currently in flight (#3512).
+    const contextTrigger = getInFlightToolCount() === 0;
     pi.sendMessage(
       {
         customType: "gsd-auto-wrapup",
@@ -308,7 +314,7 @@ export function startUnitSupervision(sctx: SupervisionContext): void {
           "Do NOT start new sub-tasks or investigations.",
         ].join("\n"),
       },
-      { triggerTurn: true },
+      { triggerTurn: contextTrigger },
     );
 
     if (s.continueHereHandle) {
diff --git a/src/resources/extensions/gsd/auto.ts b/src/resources/extensions/gsd/auto.ts
index 4fa51648e..a7cceab81 100644
--- a/src/resources/extensions/gsd/auto.ts
+++ b/src/resources/extensions/gsd/auto.ts
@@ -606,6 +606,18 @@ export async function stopAuto(
       debugLog("stop-cleanup-locks", { error: e instanceof Error ? e.message : String(e) });
     }
 
+    // ── Step 1b: Flush queued follow-up messages (#3512) ──
+    // Late async notifications (async_job_result, gsd-auto-wrapup) can trigger
+    // extra LLM turns after stop. Flush them the same way run-unit.ts does.
+    try {
+      const cmdCtxAny = s.cmdCtx as Record<string, unknown> | null;
+      if (typeof cmdCtxAny?.clearQueue === "function") {
+        (cmdCtxAny.clearQueue as () => unknown)();
+      }
+    } catch (e) {
+      debugLog("stop-cleanup-queue", { error: e instanceof Error ? e.message : String(e) });
+    }
+
     // ── Step 2: Skill state ──
     try {
       clearSkillSnapshot();
@@ -834,6 +846,19 @@ export async function pauseAuto(
 ): Promise<void> {
   if (!s.active) return;
   clearUnitTimeout();
+
+  // Flush queued follow-up messages (#3512).
+  // Late async notifications (async_job_result, gsd-auto-wrapup) can trigger
+  // extra LLM turns after pause. Flush them the same way run-unit.ts does.
+  try {
+    const cmdCtxAny = s.cmdCtx as Record<string, unknown> | null;
+    if (typeof cmdCtxAny?.clearQueue === "function") {
+      (cmdCtxAny.clearQueue as () => unknown)();
+    }
+  } catch (e) {
+    debugLog("pause-cleanup-queue", { error: e instanceof Error ? e.message : String(e) });
+  }
+
   // Unblock any pending unit promise so the auto-loop is not orphaned.
   // Pass errorContext so runUnitPhase can distinguish user-initiated pause
   // from provider-error pause and avoid hard-stopping (#2762).
diff --git a/src/resources/extensions/gsd/tests/auto-wrapup-inflight-guard.test.ts b/src/resources/extensions/gsd/tests/auto-wrapup-inflight-guard.test.ts
new file mode 100644
index 000000000..5ad5311b2
--- /dev/null
+++ b/src/resources/extensions/gsd/tests/auto-wrapup-inflight-guard.test.ts
@@ -0,0 +1,107 @@
+// GSD-2 — Regression tests for #3512: gsd-auto-wrapup mid-turn interruption
+// Copyright (c) 2026 Jeremy McSpadden <jeremy@fluxlabs.net>
+
+import { describe, test } from "node:test";
+import assert from "node:assert/strict";
+import { readFileSync } from "node:fs";
+import { join } from "node:path";
+
+const autoTimersPath = join(import.meta.dirname, "..", "auto-timers.ts");
+const autoTimersSrc = readFileSync(autoTimersPath, "utf-8");
+
+const autoPath = join(import.meta.dirname, "..", "auto.ts");
+const autoSrc = readFileSync(autoPath, "utf-8");
+
+const runUnitPath = join(import.meta.dirname, "..", "auto", "run-unit.ts");
+const runUnitSrc = readFileSync(runUnitPath, "utf-8");
+
+describe("#3512: gsd-auto-wrapup must not interrupt in-flight tool calls", () => {
+  test("soft timeout wrapup gates triggerTurn on getInFlightToolCount() === 0", () => {
+    // The soft timeout sendMessage must NOT use a hardcoded `triggerTurn: true`.
+    // It must check getInFlightToolCount() before deciding whether to trigger.
+    // Use the section marker comment to isolate the soft timeout block.
+    const startMarker = "── 1. Soft timeout warning";
+    const endMarker = "── 2. Idle watchdog";
+    const softTimeoutSection = autoTimersSrc.slice(
+      autoTimersSrc.indexOf(startMarker),
+      autoTimersSrc.indexOf(endMarker),
+    );
+    assert.ok(
+      softTimeoutSection.length > 0,
+      "Could not locate soft timeout section",
+    );
+
+    // Must reference getInFlightToolCount to gate the trigger
+    assert.ok(
+      softTimeoutSection.includes("getInFlightToolCount"),
+      "Soft timeout wrapup must gate triggerTurn behind getInFlightToolCount() check",
+    );
+
+    // Must NOT have a hardcoded triggerTurn: true
+    assert.ok(
+      !softTimeoutSection.includes("triggerTurn: true"),
+      "Soft timeout wrapup must not use hardcoded triggerTurn: true",
+    );
+  });
+
+  test("context-pressure wrapup gates triggerTurn on getInFlightToolCount() === 0", () => {
+    // The context budget sendMessage must NOT use a hardcoded `triggerTurn: true`.
+    // Use the section marker to isolate the context-pressure block.
+    const startMarker = "── 4. Context-pressure continue-here monitor";
+    const contextSection = autoTimersSrc.slice(
+      autoTimersSrc.indexOf(startMarker),
+    );
+    assert.ok(
+      contextSection.length > 0,
+      "Could not locate context budget section",
+    );
+
+    // Must reference getInFlightToolCount to gate the trigger
+    assert.ok(
+      contextSection.includes("getInFlightToolCount"),
+      "Context budget wrapup must gate triggerTurn behind getInFlightToolCount() check",
+    );
+
+    // Must NOT have a hardcoded triggerTurn: true
+    assert.ok(
+      !contextSection.includes("triggerTurn: true"),
+      "Context budget wrapup must not use hardcoded triggerTurn: true",
+    );
+  });
+});
+
+describe("#3512: pauseAuto and stopAuto must flush queued follow-up messages", () => {
+  test("stopAuto calls clearQueue()", () => {
+    // stopAuto must flush queued messages to prevent late async_job_result
+    // notifications from triggering extra LLM turns after stop.
+    const stopAutoSection = autoSrc.slice(
+      autoSrc.indexOf("export async function stopAuto("),
+      autoSrc.indexOf("export async function pauseAuto("),
+    );
+    assert.ok(stopAutoSection, "Could not locate stopAuto function");
+    assert.ok(
+      stopAutoSection.includes("clearQueue"),
+      "stopAuto must call clearQueue() to flush queued follow-up messages",
+    );
+  });
+
+  test("pauseAuto calls clearQueue()", () => {
+    // pauseAuto must also flush queued messages — same issue as stopAuto.
+    const pauseAutoSection = autoSrc.slice(
+      autoSrc.indexOf("export async function pauseAuto("),
+    );
+    assert.ok(pauseAutoSection, "Could not locate pauseAuto function");
+    assert.ok(
+      pauseAutoSection.includes("clearQueue"),
+      "pauseAuto must call clearQueue() to flush queued follow-up messages",
+    );
+  });
+
+  test("run-unit.ts still has its existing clearQueue() call (baseline)", () => {
+    // Verify the original clearQueue pattern in run-unit.ts hasn't been removed.
+    assert.ok(
+      runUnitSrc.includes("clearQueue"),
+      "run-unit.ts must retain its clearQueue() call after unit completion",
+    );
+  });
+});