diff --git a/src/agents/cli-runner.context-engine.test.ts b/src/agents/cli-runner.context-engine.test.ts
index 78293e98930c..6782f31606a8 100644
--- a/src/agents/cli-runner.context-engine.test.ts
+++ b/src/agents/cli-runner.context-engine.test.ts
@@ -175,6 +175,7 @@ describe("runPreparedCliAgent context engine lifecycle", () => {
     const dispose = vi.fn(async () => {});
     const contextEngine = createContextEngine({ bootstrap, afterTurn, maintain, dispose });
     const context = buildPreparedContext(contextEngine);
+    context.params.bootstrapContextRunKind = "heartbeat";
     const result = await runPreparedCliAgent(context);
 
     expect(result.meta.agentMeta?.sessionId).toBe("external-cli-session-1");
@@ -198,6 +199,7 @@ describe("runPreparedCliAgent context engine lifecycle", () => {
       sessionKey: "agent:main:main",
       sessionFile: "session.jsonl",
       prePromptMessageCount: 2,
+      isHeartbeat: true,
       tokenBudget: undefined,
       runtimeContext: undefined,
     });
diff --git a/src/agents/cli-runner.ts b/src/agents/cli-runner.ts
index 72aa5e1252a3..af22d2375dfe 100644
--- a/src/agents/cli-runner.ts
+++ b/src/agents/cli-runner.ts
@@ -270,6 +270,7 @@ async function finalizeCliContextEngineTurn(params: {
     sessionIdUsed: runParams.sessionId,
     sessionKey: runParams.sessionKey,
     sessionFile: runParams.sessionFile,
+    isHeartbeat: runParams.bootstrapContextRunKind === "heartbeat",
     messagesSnapshot: [...prePromptMessages, ...turnMessages],
     prePromptMessageCount: prePromptMessages.length,
     config: context.contextEngineConfig,