diff --git a/src/infra/heartbeat-runner.ts b/src/infra/heartbeat-runner.ts
index 71c41394a..5f4431722 100644
--- a/src/infra/heartbeat-runner.ts
+++ b/src/infra/heartbeat-runner.ts
@@ -35,7 +35,7 @@ import {
 } from "../config/sessions.js";
 import type { AgentDefaultsConfig } from "../config/types.agent-defaults.js";
 import { formatErrorMessage } from "../infra/errors.js";
-import { peekSystemEvents } from "../infra/system-events.js";
+import { hasSystemEvents, peekSystemEvents } from "../infra/system-events.js";
 import { createSubsystemLogger } from "../logging/subsystem.js";
 import { getQueueSize } from "../process/command-queue.js";
 import { CommandLane } from "../process/lanes.js";
@@ -460,15 +460,22 @@ export async function runHeartbeatOnce(opts: {
     return { status: "skipped", reason: "requests-in-flight" };
   }
 
+  const { entry, sessionKey, storePath } = resolveHeartbeatSession(cfg, agentId, heartbeat);
+
   // Skip heartbeat if HEARTBEAT.md exists but has no actionable content.
   // This saves API calls/costs when the file is effectively empty (only comments/headers).
-  // EXCEPTION: Don't skip for exec events - they have pending system events to process.
+  // EXCEPTION: Don't skip for exec events or if there are pending system events (from cron, etc.)
   const isExecEventReason = opts.reason === "exec-event";
+  const hasPendingSystemEvents = hasSystemEvents(sessionKey);
   const workspaceDir = resolveAgentWorkspaceDir(cfg, agentId);
   const heartbeatFilePath = path.join(workspaceDir, DEFAULT_HEARTBEAT_FILENAME);
   try {
     const heartbeatFileContent = await fs.readFile(heartbeatFilePath, "utf-8");
-    if (isHeartbeatContentEffectivelyEmpty(heartbeatFileContent) && !isExecEventReason) {
+    if (
+      isHeartbeatContentEffectivelyEmpty(heartbeatFileContent) &&
+      !isExecEventReason &&
+      !hasPendingSystemEvents
+    ) {
       emitHeartbeatEvent({
         status: "skipped",
         reason: "empty-heartbeat-file",
@@ -480,8 +487,6 @@ export async function runHeartbeatOnce(opts: {
     // File doesn't exist or can't be read - proceed with heartbeat.
     // The LLM prompt says "if it exists" so this is expected behavior.
   }
-
-  const { entry, sessionKey, storePath } = resolveHeartbeatSession(cfg, agentId, heartbeat);
   const previousUpdatedAt = entry?.updatedAt;
   const delivery = resolveHeartbeatDeliveryTarget({ cfg, entry, heartbeat });
   const visibility =