diff --git a/extensions/guardian/message-cache.test.ts b/extensions/guardian/message-cache.test.ts
index ee025d21c41..d1b93d50d8c 100644
--- a/extensions/guardian/message-cache.test.ts
+++ b/extensions/guardian/message-cache.test.ts
@@ -556,12 +556,12 @@ describe("message-cache", () => {
       expect(isSystemTrigger("nonexistent")).toBe(false);
     });
 
-    it("preserves isSystemTrigger when subsequent llm_input has no prompt", () => {
+    it("stays true when heartbeat is in historyMessages on subsequent llm_input", () => {
       // Heartbeat fires with prompt → isSystemTrigger=true
       updateCache("s1", [], "heartbeat", 3, NO_FILTER);
       expect(isSystemTrigger("s1")).toBe(true);
 
-      // Agent loop continues without prompt (tool result processed) → should preserve true
+      // Agent loop continues — heartbeat is now in historyMessages
       updateCache("s1", [{ role: "user", content: "heartbeat" }], undefined, 3, NO_FILTER);
       expect(isSystemTrigger("s1")).toBe(true);
     });
@@ -570,11 +570,15 @@ describe("message-cache", () => {
       updateCache("s1", [], "heartbeat", 3, NO_FILTER);
       expect(isSystemTrigger("s1")).toBe(true);
 
-      // Real user message arrives → should reset to false
+      // Real user message arrives — now the last user message in history is the real one
       updateCache(
         "s1",
-        [{ role: "user", content: "heartbeat" }],
-        "Deploy my project",
+        [
+          { role: "user", content: "heartbeat" },
+          { role: "assistant", content: "HEARTBEAT_OK" },
+          { role: "user", content: "Deploy my project" },
+        ],
+        undefined,
         3,
         NO_FILTER,
       );
@@ -586,6 +590,27 @@ describe("message-cache", () => {
       updateCache("s1", [], undefined, 3, NO_FILTER);
       expect(isSystemTrigger("s1")).toBe(false);
     });
+
+    it("detects heartbeat from last user message in historyMessages when currentPrompt is undefined", () => {
+      // Heartbeat prompt arrives via historyMessages, not currentPrompt
+      const heartbeatPrompt =
+        "Read HEARTBEAT.md if it exists (workspace context). If nothing needs attention, reply HEARTBEAT_OK.";
+      updateCache("s1", [{ role: "user", content: heartbeatPrompt }], undefined, 3, NO_FILTER);
+      expect(isSystemTrigger("s1")).toBe(true);
+    });
+
+    it("detects heartbeat from historyMessages even on first llm_input (no existing entry)", () => {
+      updateCache("s1", [{ role: "user", content: "heartbeat" }], undefined, 3, NO_FILTER);
+      expect(isSystemTrigger("s1")).toBe(true);
+    });
+
+    it("resets when historyMessages last user message is not a system trigger", () => {
+      updateCache("s1", [{ role: "user", content: "heartbeat" }], undefined, 3, NO_FILTER);
+      expect(isSystemTrigger("s1")).toBe(true);
+
+      updateCache("s1", [{ role: "user", content: "Deploy my project" }], undefined, 3, NO_FILTER);
+      expect(isSystemTrigger("s1")).toBe(false);
+    });
   });
 
   describe("getRecentTurns filters system turns", () => {
diff --git a/extensions/guardian/message-cache.ts b/extensions/guardian/message-cache.ts
index 371c17330bf..a236e4bf35f 100644
--- a/extensions/guardian/message-cache.ts
+++ b/extensions/guardian/message-cache.ts
@@ -49,14 +49,13 @@ export function updateCache(
     contextTools,
     totalTurnsProcessed: totalTurns,
     lastSummarizedTurnCount: existing?.lastSummarizedTurnCount ?? 0,
-    // Preserve isSystemTrigger when currentPrompt is empty (agent loop continuation).
-    // During a heartbeat cycle, llm_input fires multiple times: first with the
-    // heartbeat prompt (isSystemTrigger=true), then without a prompt as the agent
-    // loop continues after tool results. Without preservation, the flag resets to
-    // false and heartbeat tool calls reach the guardian unnecessarily.
-    isSystemTrigger: currentPrompt
-      ? isSystemTriggerPrompt(currentPrompt)
-      : (existing?.isSystemTrigger ?? false),
+    // Detect system triggers from both currentPrompt AND the last user message
+    // in historyMessages. Heartbeats may arrive via either path depending on
+    // the agent loop stage (currentPrompt on first llm_input, historyMessages
+    // on subsequent continuations after tool results).
+    isSystemTrigger:
+      isSystemTriggerPrompt(currentPrompt) ||
+      isSystemTriggerPrompt(getLastUserMessageText(historyMessages)),
     agentSystemPrompt: existing?.agentSystemPrompt,
     updatedAt: Date.now(),
   });
@@ -279,6 +278,17 @@ function filterSystemTurns(turns: ConversationTurn[]): ConversationTurn[] {
   });
 }
 
+/** Extract text from the last user message in the history array. */
+function getLastUserMessageText(historyMessages: unknown[]): string | undefined {
+  for (let i = historyMessages.length - 1; i >= 0; i--) {
+    const msg = historyMessages[i];
+    if (isMessageLike(msg) && msg.role === "user") {
+      return extractTextContent(msg.content) || undefined;
+    }
+  }
+  return undefined;
+}
+
 /** Count user messages in the history array. */
 function countUserMessages(historyMessages: unknown[]): number {
   let count = 0;