diff --git a/server/src/__tests__/heartbeat-process-recovery.test.ts b/server/src/__tests__/heartbeat-process-recovery.test.ts
index e1065ae4f18..6e47ecc3c68 100644
--- a/server/src/__tests__/heartbeat-process-recovery.test.ts
+++ b/server/src/__tests__/heartbeat-process-recovery.test.ts
@@ -43,6 +43,7 @@ import {
 import { runningProcesses } from "../adapters/index.ts";
 const mockTelemetryClient = vi.hoisted(() => ({ track: vi.fn() }));
 const mockTrackAgentFirstHeartbeat = vi.hoisted(() => vi.fn());
+const mockTerminateLocalService = vi.hoisted(() => vi.fn());
 const mockAdapterExecute = vi.hoisted(() =>
   vi.fn(async () => ({
     exitCode: 0,
@@ -59,6 +60,17 @@ vi.mock("../telemetry.ts", () => ({
   getTelemetryClient: () => mockTelemetryClient,
 }));
 
+vi.mock("../services/local-service-supervisor.js", async () => {
+  const actual = await vi.importActual<typeof import("../services/local-service-supervisor.js")>(
+    "../services/local-service-supervisor.js",
+  );
+  mockTerminateLocalService.mockImplementation(actual.terminateLocalService);
+  return {
+    ...actual,
+    terminateLocalService: mockTerminateLocalService,
+  };
+});
+
 vi.mock("@paperclipai/shared/telemetry", async () => {
   const actual = await vi.importActual<typeof import("@paperclipai/shared/telemetry")>(
     "@paperclipai/shared/telemetry",
@@ -277,6 +289,10 @@ describeEmbeddedPostgres("heartbeat orphaned process recovery", () => {
 
   afterEach(async () => {
     vi.clearAllMocks();
+    const localServiceSupervisor = await vi.importActual<typeof import("../services/local-service-supervisor.js")>(
+      "../services/local-service-supervisor.js",
+    );
+    mockTerminateLocalService.mockImplementation(localServiceSupervisor.terminateLocalService);
     mockAdapterExecute.mockImplementation(async () => ({
       exitCode: 0,
       signal: null,
@@ -1893,6 +1909,35 @@ describeEmbeddedPostgres("heartbeat orphaned process recovery", () => {
     );
   });
 
+  it("terminates the in-memory process before persisting cancellation status", async () => {
+    const { runId } = await seedRunFixture({
+      agentStatus: "running",
+      includeIssue: false,
+    });
+    const heartbeat = heartbeatService(db);
+    runningProcesses.set(runId, {
+      child: { pid: 12345 } as ChildProcess,
+      graceSec: 1,
+      processGroupId: null,
+    });
+    mockTerminateLocalService.mockResolvedValueOnce(undefined);
+    const updateSpy = vi.spyOn(db, "update");
+    updateSpy.mockImplementationOnce((() => {
+      throw new Error("db update unavailable");
+    }) as typeof db.update);
+
+    try {
+      await expect(heartbeat.cancelRun(runId)).rejects.toThrow("db update unavailable");
+      expect(mockTerminateLocalService).toHaveBeenCalledWith(
+        expect.objectContaining({ pid: 12345, processGroupId: null }),
+        { forceAfterMs: 1000 },
+      );
+      expect(runningProcesses.has(runId)).toBe(false);
+    } finally {
+      updateSpy.mockRestore();
+    }
+  });
+
   it("records manual cancellation stop metadata", async () => {
     const { runId } = await seedRunFixture({
       agentStatus: "running",
diff --git a/server/src/services/heartbeat.ts b/server/src/services/heartbeat.ts
index 79a321e422d..910d395a4cd 100644
--- a/server/src/services/heartbeat.ts
+++ b/server/src/services/heartbeat.ts
@@ -10636,32 +10636,37 @@ export function heartbeatService(db: Db, options: HeartbeatServiceOptions = {})
         }
       : options.resultJson;
 
+    const running = runningProcesses.get(run.id);
+    try {
+      if (running) {
+        await terminateHeartbeatRunProcess({
+          pid: running.child.pid ?? run.processPid,
+          processGroupId: running.processGroupId ?? run.processGroupId,
+          graceMs: Math.max(1, running.graceSec) * 1000,
+        });
+      } else if (run.processPid || run.processGroupId) {
+        await terminateHeartbeatRunProcess({
+          pid: run.processPid,
+          processGroupId: run.processGroupId,
+        });
+      }
+    } finally {
+      runningProcesses.delete(run.id);
+    }
+
+    const finishedAt = new Date();
     const cancelled = await setRunStatus(run.id, "cancelled", {
-      finishedAt: new Date(),
+      finishedAt,
       error: reason,
       errorCode,
       ...(resultJson ? { resultJson } : {}),
     });
 
     await setWakeupStatus(run.wakeupRequestId, "cancelled", {
-      finishedAt: new Date(),
+      finishedAt,
       error: reason,
     });
 
-    const running = runningProcesses.get(run.id);
-    if (running) {
-      await terminateHeartbeatRunProcess({
-        pid: running.child.pid ?? run.processPid,
-        processGroupId: running.processGroupId ?? run.processGroupId,
-        graceMs: Math.max(1, running.graceSec) * 1000,
-      });
-    } else if (run.processPid || run.processGroupId) {
-      await terminateHeartbeatRunProcess({
-        pid: run.processPid,
-        processGroupId: run.processGroupId,
-      });
-    }
-
     if (cancelled) {
       await appendRunEvent(cancelled, 1, {
         eventType: "lifecycle",
@@ -10673,7 +10678,6 @@ export function heartbeatService(db: Db, options: HeartbeatServiceOptions = {})
       await releaseIssueExecutionAndPromote(cancelled);
     }
 
-    runningProcesses.delete(run.id);
     await finalizeAgentStatus(run.agentId, "cancelled");
     await startNextQueuedRunForAgent(run.agentId);
     return cancelled;