diff --git a/apps/readest-app/src/__tests__/utils/annotator-util.test.ts b/apps/readest-app/src/__tests__/utils/annotator-util.test.ts
index 3b50818a..3882f75b 100644
--- a/apps/readest-app/src/__tests__/utils/annotator-util.test.ts
+++ b/apps/readest-app/src/__tests__/utils/annotator-util.test.ts
@@ -2,11 +2,13 @@ import { describe, it, expect, vi } from 'vitest';
 import {
   getExternalDragHandle,
   getHighlightColorLabel,
+  removeBookNoteOverlays,
   toParentViewportPoint,
 } from '@/app/reader/utils/annotatorUtil';
 import { Point } from '@/utils/sel';
-import { UserHighlightColor } from '@/types/book';
+import { BookNote, UserHighlightColor } from '@/types/book';
 import { SystemSettings } from '@/types/settings';
+import { FoliateView, NOTE_PREFIX } from '@/types/view';
 
 describe('getExternalDragHandle', () => {
   const currentStart: Point = { x: 100, y: 200 };
@@ -140,3 +142,86 @@ describe('getHighlightColorLabel', () => {
     expect(getHighlightColorLabel(settings, 'red')).toBeUndefined();
   });
 });
+
+describe('removeBookNoteOverlays', () => {
+  const makeView = () => {
+    const addAnnotation = vi.fn();
+    const view = { addAnnotation } as unknown as FoliateView;
+    return { view, addAnnotation };
+  };
+
+  const baseNote = (overrides: Partial<BookNote> = {}): BookNote => ({
+    id: 'id-1',
+    type: 'annotation',
+    cfi: 'epubcfi(/6/4!/4/2)',
+    note: '',
+    createdAt: 1,
+    updatedAt: 1,
+    ...overrides,
+  });
+
+  it('removes only the highlight overlay for a highlight-only annotation', () => {
+    const { view, addAnnotation } = makeView();
+    const note = baseNote({ style: 'highlight', color: 'yellow' });
+
+    removeBookNoteOverlays(view, note);
+
+    expect(addAnnotation).toHaveBeenCalledTimes(1);
+    expect(addAnnotation).toHaveBeenCalledWith(expect.objectContaining({ value: note.cfi }), true);
+    const passed = addAnnotation.mock.calls[0]![0] as BookNote & { value: string };
+    expect(passed.value.startsWith(NOTE_PREFIX)).toBe(false);
+  });
+
+  it('removes only the note overlay for a note-only annotation', () => {
+    const { view, addAnnotation } = makeView();
+    const note = baseNote({ note: 'my comment' });
+
+    removeBookNoteOverlays(view, note);
+
+    expect(addAnnotation).toHaveBeenCalledTimes(1);
+    expect(addAnnotation).toHaveBeenCalledWith(
+      expect.objectContaining({ value: `${NOTE_PREFIX}${note.cfi}` }),
+      true,
+    );
+  });
+
+  it('removes both overlays when the annotation has a highlight and a note', () => {
+    const { view, addAnnotation } = makeView();
+    const note = baseNote({ style: 'underline', color: 'red', note: 'my comment' });
+
+    removeBookNoteOverlays(view, note);
+
+    expect(addAnnotation).toHaveBeenCalledTimes(2);
+    const values = addAnnotation.mock.calls.map(
+      (call) => (call[0] as BookNote & { value: string }).value,
+    );
+    expect(values).toContain(note.cfi);
+    expect(values).toContain(`${NOTE_PREFIX}${note.cfi}`);
+    for (const call of addAnnotation.mock.calls) {
+      expect(call[1]).toBe(true);
+    }
+  });
+
+  it('does nothing for a bookmark (no highlight, no note text)', () => {
+    const { view, addAnnotation } = makeView();
+    const bookmark = baseNote({ type: 'bookmark' });
+
+    removeBookNoteOverlays(view, bookmark);
+
+    expect(addAnnotation).not.toHaveBeenCalled();
+  });
+
+  it('treats whitespace-only note text as empty and skips the note overlay', () => {
+    const { view, addAnnotation } = makeView();
+    const note = baseNote({ style: 'highlight', note: '   \n  ' });
+
+    removeBookNoteOverlays(view, note);
+
+    expect(addAnnotation).toHaveBeenCalledTimes(1);
+    expect(addAnnotation).toHaveBeenCalledWith(expect.objectContaining({ value: note.cfi }), true);
+  });
+
+  it('is a no-op when view is null', () => {
+    expect(() => removeBookNoteOverlays(null, baseNote({ style: 'highlight' }))).not.toThrow();
+  });
+});
diff --git a/apps/readest-app/src/app/reader/components/sidebar/BooknoteItem.tsx b/apps/readest-app/src/app/reader/components/sidebar/BooknoteItem.tsx
index 3b037551..2d9874ac 100644
--- a/apps/readest-app/src/app/reader/components/sidebar/BooknoteItem.tsx
+++ b/apps/readest-app/src/app/reader/components/sidebar/BooknoteItem.tsx
@@ -13,7 +13,7 @@ import { useBookDataStore } from '@/store/bookDataStore';
 import { useTranslation } from '@/hooks/useTranslation';
 import { useResponsiveSize } from '@/hooks/useResponsiveSize';
 import { eventDispatcher } from '@/utils/event';
-import { NOTE_PREFIX } from '@/types/view';
+import { removeBookNoteOverlays } from '../../utils/annotatorUtil';
 import useScrollToItem from '../../hooks/useScrollToItem';
 import TextButton from '@/components/TextButton';
 import TextEditor, { TextEditorRef } from '@/components/TextEditor';
@@ -66,9 +66,7 @@ const BooknoteItem: React.FC<BooknoteItemProps> = ({ bookKey, item, isNearest, o
       if (item.id === note.id) {
         item.deletedAt = Date.now();
         const views = getViewsById(bookKey.split('-')[0]!);
-        views.forEach((view) =>
-          view?.addAnnotation({ ...item, value: `${NOTE_PREFIX}${item.cfi}` }, true),
-        );
+        views.forEach((view) => removeBookNoteOverlays(view, item));
       }
     });
     const updatedConfig = updateBooknotes(bookKey, booknotes);
diff --git a/apps/readest-app/src/app/reader/utils/annotatorUtil.ts b/apps/readest-app/src/app/reader/utils/annotatorUtil.ts
index f8943d93..26143930 100644
--- a/apps/readest-app/src/app/reader/utils/annotatorUtil.ts
+++ b/apps/readest-app/src/app/reader/utils/annotatorUtil.ts
@@ -1,6 +1,7 @@
 import { HIGHLIGHT_COLOR_HEX } from '@/services/constants';
-import { DEFAULT_HIGHLIGHT_COLORS, HighlightColor } from '@/types/book';
+import { BookNote, DEFAULT_HIGHLIGHT_COLORS, HighlightColor } from '@/types/book';
 import { SystemSettings } from '@/types/settings';
+import { FoliateView, NOTE_PREFIX } from '@/types/view';
 import { Point } from '@/utils/sel';
 
 export const isDefaultHighlightColor = (
@@ -62,3 +63,26 @@ export function toParentViewportPoint(doc: Document, x: number, y: number): Poin
   const frameRect = frameElement?.getBoundingClientRect() ?? { top: 0, left: 0 };
   return { x: x + frameRect.left, y: y + frameRect.top };
 }
+
+/**
+ * Remove any overlays drawn for a BookNote from the given view.
+ *
+ * A single BookNote can have up to two overlays attached:
+ *   - a highlight/underline/squiggly overlay (keyed by the raw CFI)
+ *   - a note bubble overlay (keyed by `${NOTE_PREFIX}${cfi}`)
+ *
+ * The set of overlays drawn is defined by the progress-sync effect in
+ * Annotator.tsx, and this helper mirrors those filters so that deleting
+ * an annotation from the sidebar clears every overlay that was drawn
+ * for it, not just the note bubble.
+ */
+export function removeBookNoteOverlays(view: FoliateView | null, note: BookNote): void {
+  if (!view) return;
+  if (note.type !== 'annotation') return;
+  if (note.style) {
+    view.addAnnotation({ ...note, value: note.cfi }, true);
+  }
+  if (note.note && note.note.trim().length > 0) {
+    view.addAnnotation({ ...note, value: `${NOTE_PREFIX}${note.cfi}` }, true);
+  }
+}