diff --git a/packages/ui/src/lib/persistence.test.ts b/packages/ui/src/lib/persistence.test.ts
index ff72c1b8..c698f711 100644
--- a/packages/ui/src/lib/persistence.test.ts
+++ b/packages/ui/src/lib/persistence.test.ts
@@ -641,6 +641,43 @@ describe('updateDesktopSettings', () => {
     }
   });
 
+  test('preserves only the latest settings values across repeated pending updates', async () => {
+    const loadedSettings = deferred<{ settings: SettingsPayload; source: 'web' | 'vscode' }>();
+    registerSettingsApi(async (changes) => changes as SettingsPayload, () => loadedSettings.promise);
+    invalidateSettingsCache();
+    const syncedSettings: SettingsPayload[] = [];
+    const handleSettingsSynced = (event: Event) => {
+      syncedSettings.push((event as CustomEvent<SettingsPayload>).detail);
+    };
+    getWindow().addEventListener('openchamber:settings-synced', handleSettingsSynced);
+
+    try {
+      const sync = syncDesktopSettings();
+      const updates = Array.from({ length: 100 }, (_, index) => updateDesktopSettings({
+        activeProjectId: `project-${index}`,
+        showReasoningTraces: index % 2 === 0,
+      }));
+
+      loadedSettings.resolve({
+        settings: {
+          activeProjectId: 'stale-project',
+          showReasoningTraces: true,
+          draftStartersCraftGoalAdded: true,
+          draftStartersScheduleTaskAdded: true,
+        },
+        source: 'web',
+      });
+      await sync;
+
+      expect(syncedSettings.at(-1)?.activeProjectId).toBe('project-99');
+      expect(syncedSettings.at(-1)?.showReasoningTraces).toBe(false);
+
+      await Promise.all(updates);
+    } finally {
+      getWindow().removeEventListener('openchamber:settings-synced', handleSettingsSynced);
+    }
+  });
+
   test('applies model selector settings from server settings', async () => {
     getWindow();
     const settings = {
diff --git a/packages/ui/src/lib/persistence.ts b/packages/ui/src/lib/persistence.ts
index ea9fef52..898ff502 100644
--- a/packages/ui/src/lib/persistence.ts
+++ b/packages/ui/src/lib/persistence.ts
@@ -1679,7 +1679,19 @@ class SettingsMutationTracker {
 
   record(changes: Partial<DesktopSettings>): number {
     this.revision += 1;
-    this.mutations.push({ revision: this.revision, changes });
+    if (this.operations.size > 0) {
+      const latest = this.mutations.at(-1);
+      // A new segment is only needed when an operation started after the last one.
+      const crossedOperationBoundary = latest
+        ? [...this.operations].some((operation) => operation.revision >= latest.revision)
+        : true;
+      if (latest && !crossedOperationBoundary) {
+        latest.revision = this.revision;
+        latest.changes = { ...latest.changes, ...changes };
+      } else {
+        this.mutations.push({ revision: this.revision, changes });
+      }
+    }
     return this.revision;
   }