diff --git a/server/src/__tests__/heartbeat-worktree-suppression.test.ts b/server/src/__tests__/heartbeat-worktree-suppression.test.ts
index dc2ed876e08..9e12c5f5c40 100644
--- a/server/src/__tests__/heartbeat-worktree-suppression.test.ts
+++ b/server/src/__tests__/heartbeat-worktree-suppression.test.ts
@@ -170,6 +170,50 @@ describeEmbeddedPostgres("heartbeat worktree suppression", () => {
     });
   });
 
+  it("counts quarantined runs only for the active seed epoch", async () => {
+    const { companyId, agentId, issueId } = await insertAgentAndIssue();
+    const settings = instanceSettingsService(db, {
+      runtimeEnv: {
+        PAPERCLIP_IN_WORKTREE: "true",
+        PAPERCLIP_INSTANCE_ID: "test-worktree",
+      },
+    });
+    const experimental = await settings.getExperimental();
+    const activeSeedEpoch = experimental.worktreeRunExecutionSeedEpoch;
+    expect(activeSeedEpoch).not.toBeNull();
+
+    await db.insert(heartbeatRuns).values([
+      {
+        id: randomUUID(),
+        companyId,
+        agentId,
+        seedEpoch: activeSeedEpoch,
+        invocationSource: "assignment",
+        triggerDetail: "system",
+        status: "cancelled",
+        errorCode: "worktree_seed_quarantine",
+        responsibleUserId: "responsible-user",
+        contextSnapshot: { issueId },
+      },
+      {
+        id: randomUUID(),
+        companyId,
+        agentId,
+        seedEpoch: randomUUID(),
+        invocationSource: "assignment",
+        triggerDetail: "system",
+        status: "cancelled",
+        errorCode: "worktree_seed_quarantine",
+        responsibleUserId: "responsible-user",
+        contextSnapshot: { issueId },
+      },
+    ]);
+
+    await expect(settings.getWorktreeRunEngineStatus()).resolves.toMatchObject({
+      quarantinedRunCount: 1,
+    });
+  });
+
   async function waitForCompletedRun(runId: string, agentId: string) {
     let latestStatus: string | null = null;
     let latestLastRunId: string | null = null;
diff --git a/server/src/services/instance-settings.ts b/server/src/services/instance-settings.ts
index b13d934c533..f97adcf3a2e 100644
--- a/server/src/services/instance-settings.ts
+++ b/server/src/services/instance-settings.ts
@@ -503,11 +503,16 @@ export function instanceSettingsService(db: Db, options: InstanceSettingsService
       // Only quarantined-run rows survive a seed (P1 deletes the wakeups/monitors
       // it clears), so this count is the durable evidence of what was neutralized.
       let quarantinedRunCount = 0;
-      if (inWorktree) {
+      if (inWorktree && experimental.worktreeRunExecutionSeedEpoch) {
         const [row] = await db
           .select({ count: sql<number>`count(*)::int` })
           .from(heartbeatRuns)
-          .where(eq(heartbeatRuns.errorCode, WORKTREE_SEED_QUARANTINE_ERROR_CODE));
+          .where(
+            and(
+              eq(heartbeatRuns.errorCode, WORKTREE_SEED_QUARANTINE_ERROR_CODE),
+              eq(heartbeatRuns.seedEpoch, experimental.worktreeRunExecutionSeedEpoch),
+            ),
+          );
         quarantinedRunCount = row?.count ?? 0;
       }
       return {