diff --git a/server/src/__tests__/heartbeat-direct-adapter-native-isolation.test.ts b/server/src/__tests__/heartbeat-direct-adapter-native-isolation.test.ts
index 13a0090c5a..1c80057966 100644
--- a/server/src/__tests__/heartbeat-direct-adapter-native-isolation.test.ts
+++ b/server/src/__tests__/heartbeat-direct-adapter-native-isolation.test.ts
@@ -6,6 +6,7 @@ import {
   companies,
   completionContracts,
   createDb,
+  heartbeatRuns,
   nativeRunFinalizations,
   nativeRunResults,
   statusDecisions,
@@ -16,6 +17,7 @@ import {
   getEmbeddedPostgresTestSupport,
   startEmbeddedPostgresTestDatabase,
 } from "./helpers/embedded-postgres.js";
+import { drainHeartbeatRunsToQuiescence } from "./helpers/drain-heartbeat-runs.js";
 import {
   registerServerAdapter,
   unregisterServerAdapter,
@@ -52,12 +54,14 @@ async function waitForRunToFinish(
 
 describeEmbeddedPostgres("direct adapter native-runner isolation", () => {
   let db!: ReturnType<typeof createDb>;
+  let heartbeat!: ReturnType<typeof heartbeatService>;
   let tempDb: Awaited<ReturnType<typeof startEmbeddedPostgresTestDatabase>> | null = null;
   const execute = vi.fn<ServerAdapterModule["execute"]>();
 
   beforeAll(async () => {
     tempDb = await startEmbeddedPostgresTestDatabase("heartbeat-direct-adapter-isolation-");
     db = createDb(tempDb.connectionString);
+    heartbeat = heartbeatService(db);
     for (const [adapterType] of DIRECT_ADAPTERS) {
       registerServerAdapter({
         type: adapterType,
@@ -74,6 +78,12 @@ describeEmbeddedPostgres("direct adapter native-runner isolation", () => {
   }, 20_000);
 
   afterEach(async () => {
+    await drainHeartbeatRunsToQuiescence(db, heartbeat);
+    const runStatuses = await db.select({ status: heartbeatRuns.status }).from(heartbeatRuns);
+    const pendingRuns = runStatuses.filter(
+      (run) => run.status === "queued" || run.status === "running",
+    );
+    expect(pendingRuns).toEqual([]);
     vi.clearAllMocks();
     await db.execute(sql.raw(`
       TRUNCATE TABLE
@@ -97,6 +107,7 @@ describeEmbeddedPostgres("direct adapter native-runner isolation", () => {
   });
 
   afterAll(async () => {
+    await heartbeat.drainActiveRunExecutions();
     for (const [adapterType] of DIRECT_ADAPTERS) {
       unregisterServerAdapter(adapterType);
     }
@@ -138,7 +149,6 @@ describeEmbeddedPostgres("direct adapter native-runner isolation", () => {
         permissions: {},
       });
 
-      const heartbeat = heartbeatService(db);
       const queued = await heartbeat.invoke(agentId, "on_demand", {}, "manual");
       expect(queued).not.toBeNull();
       const finished = await waitForRunToFinish(heartbeat, queued!.id);