diff --git a/apps/readest-app/src/__tests__/utils/serializer.test.ts b/apps/readest-app/src/__tests__/utils/serializer.test.ts
index ca958664..4117ddb9 100644
--- a/apps/readest-app/src/__tests__/utils/serializer.test.ts
+++ b/apps/readest-app/src/__tests__/utils/serializer.test.ts
@@ -108,6 +108,43 @@ describe('BookConfig serialization', () => {
     expect(tombstone.deletedAt).toBeTruthy();
   });
 
+  it('does not persist an array view setting that equals the global value', () => {
+    // Array/object view settings must be compared by value, not reference —
+    // otherwise annotationToolbarItems (an array) is stored as a per-book override on
+    // every save, shadowing later global changes (the customize-toolbar bug).
+    const global = {
+      ...globalViewSettings,
+      annotationToolbarItems: ['highlight', 'annotate', 'copy'],
+    } as unknown as ViewSettings;
+    const config: BookConfig = {
+      updatedAt: 1,
+      // Same content as global but a distinct array reference, as produced by the
+      // load -> merge -> serialize round-trip.
+      viewSettings: {
+        annotationToolbarItems: ['highlight', 'annotate', 'copy'],
+      } as Partial<ViewSettings>,
+    };
+
+    const parsed = JSON.parse(serializeConfig(config, global, defaultSearchConfig));
+
+    expect(parsed.viewSettings.annotationToolbarItems).toBeUndefined();
+  });
+
+  it('persists an array view setting that differs from the global value', () => {
+    const global = {
+      ...globalViewSettings,
+      annotationToolbarItems: ['highlight', 'annotate', 'copy'],
+    } as unknown as ViewSettings;
+    const config: BookConfig = {
+      updatedAt: 1,
+      viewSettings: { annotationToolbarItems: ['copy'] } as Partial<ViewSettings>,
+    };
+
+    const parsed = JSON.parse(serializeConfig(config, global, defaultSearchConfig));
+
+    expect(parsed.viewSettings.annotationToolbarItems).toEqual(['copy']);
+  });
+
   it('does not migrate annotations when schemaVersion is already 2', () => {
     const config = deserializeConfig(
       JSON.stringify({
diff --git a/apps/readest-app/src/utils/serializer.ts b/apps/readest-app/src/utils/serializer.ts
index 615f0a24..e2531fc5 100644
--- a/apps/readest-app/src/utils/serializer.ts
+++ b/apps/readest-app/src/utils/serializer.ts
@@ -14,6 +14,15 @@ export const serializeRawConfig = (config: Partial<BookConfig>): string => {
   return JSON.stringify(stampBookConfigSchema(config));
 };
 
+// Compare a per-book view-setting value with the global one by value, not
+// reference. serializeConfig deep-clones the config first, so array/object
+// settings (e.g. annotationToolbarItems) are always fresh references; a reference
+// check would persist them as per-book overrides even when identical to global,
+// which then shadows later global changes on reopen. Primitives short-circuit;
+// the JSON compare covers arrays and plain config objects (all JSON-serializable).
+const isSameViewSettingValue = (a: unknown, b: unknown): boolean =>
+  a === b || JSON.stringify(a) === JSON.stringify(b);
+
 export const serializeConfig = (
   config: BookConfig,
   globalViewSettings: ViewSettings,
@@ -35,7 +44,7 @@ export const serializeConfig = (
   const searchConfig = (config.searchConfig ?? {}) as Partial<BookSearchConfig>;
   config.viewSettings = Object.entries(viewSettings).reduce(
     (acc: Partial<Record<keyof ViewSettings, unknown>>, [key, value]) => {
-      if (globalViewSettings[key as keyof ViewSettings] !== value) {
+      if (!isSameViewSettingValue(globalViewSettings[key as keyof ViewSettings], value)) {
         acc[key as keyof ViewSettings] = value;
       }
       return acc;