diff --git a/src/config/legacy-migrate.test.ts b/src/config/legacy-migrate.test.ts
index 94182b41e63e..1e19f15e550d 100644
--- a/src/config/legacy-migrate.test.ts
+++ b/src/config/legacy-migrate.test.ts
@@ -208,6 +208,16 @@ describe("legacy migrate heartbeat config", () => {
     expect((res.config as { heartbeat?: unknown } | null)?.heartbeat).toBeUndefined();
     expect((res.config as { agent?: unknown } | null)?.agent).toBeUndefined();
   });
+
+  it("records a migration change when removing empty top-level heartbeat", () => {
+    const res = migrateLegacyConfig({
+      heartbeat: {},
+    });
+
+    expect(res.changes).toContain("Removed empty top-level heartbeat.");
+    expect(res.config).not.toBeNull();
+    expect((res.config as { heartbeat?: unknown } | null)?.heartbeat).toBeUndefined();
+  });
 });
 
 describe("legacy migrate controlUi.allowedOrigins seed (issue #29385)", () => {
diff --git a/src/config/legacy.migrations.part-3.ts b/src/config/legacy.migrations.part-3.ts
index dbc097480e50..db4d3a9c9f9e 100644
--- a/src/config/legacy.migrations.part-3.ts
+++ b/src/config/legacy.migrations.part-3.ts
@@ -343,6 +343,9 @@ export const LEGACY_CONFIG_MIGRATIONS_PART_3: LegacyConfigMigration[] = [
         raw.channels = channels;
       }
 
+      if (!agentHeartbeat && !channelHeartbeat) {
+        changes.push("Removed empty top-level heartbeat.");
+      }
       delete raw.heartbeat;
     },
   },