diff --git a/server/src/modules/file-write/formats/audio/audio-metadata-embedder.test.ts b/server/src/modules/file-write/formats/audio/audio-metadata-embedder.test.ts
index 733bff832..da10972e7 100644
--- a/server/src/modules/file-write/formats/audio/audio-metadata-embedder.test.ts
+++ b/server/src/modules/file-write/formats/audio/audio-metadata-embedder.test.ts
@@ -213,10 +213,18 @@ describe('AudioMetadataEmbedder', () => {
   it('adds MP3-specific ID3v2 compatibility args', () => {
     const args = testing.buildFfmpegArgs('/books/audio/book.mp3', '/books/audio/cover.jpg', '/books/audio/out.mp3', 'mp3', []);
 
+    expect(args).toContain('-copyts');
+    expect(args.indexOf('-copyts')).toBeLessThan(args.indexOf('-i'));
     expect(args).toContain('-id3v2_version');
     expect(args[args.indexOf('-id3v2_version') + 1]).toBe('3');
   });
 
+  it.each(['m4b', 'm4a', 'flac'])('does not add MP3 timestamp handling to %s output', (format) => {
+    const args = testing.buildFfmpegArgs(`/books/audio/book.${format}`, null, `/books/audio/out.${format}`, format, []);
+
+    expect(args).not.toContain('-copyts');
+  });
+
   it.each(['m4b', 'm4a'])('enables extended metadata tags for %s output', (format) => {
     const args = testing.buildFfmpegArgs('/books/audio/book.m4b', null, `/books/audio/out.${format}`, format, [{ key: 'series', value: 'Series' }]);
 
diff --git a/server/src/modules/file-write/formats/audio/audio-metadata-embedder.ts b/server/src/modules/file-write/formats/audio/audio-metadata-embedder.ts
index 2ad2e7adf..67acf0318 100644
--- a/server/src/modules/file-write/formats/audio/audio-metadata-embedder.ts
+++ b/server/src/modules/file-write/formats/audio/audio-metadata-embedder.ts
@@ -113,7 +113,14 @@ function buildFfmpegArgs(
   metadata: AudioMetadataArg[],
   options?: { useMp4MetadataTags?: boolean; muxer?: string; chaptersPath?: string | null },
 ): string[] {
-  const args = ['-v', 'error', '-y', '-i', filePath];
+  const normalizedFormat = format.toLowerCase();
+  const args = ['-v', 'error', '-y'];
+  if (normalizedFormat === FORMAT_MP3) {
+    // MP3 encoder delay gives the input a positive start time that FFmpeg otherwise subtracts
+    // from carried chapters on every remux.
+    args.push('-copyts');
+  }
+  args.push('-i', filePath);
   const chaptersPath = options?.chaptersPath ?? null;
 
   if (coverPath) {
@@ -134,7 +141,7 @@ function buildFfmpegArgs(
   const chaptersInput = chaptersPath ? (coverPath ? 2 : 1) : 0;
   args.push('-map_metadata', '0', '-map_chapters', String(chaptersInput), '-c', 'copy');
 
-  if (format.toLowerCase() === FORMAT_MP3) {
+  if (normalizedFormat === FORMAT_MP3) {
     args.push('-id3v2_version', '3');
   }
 
diff --git a/server/src/modules/file-write/formats/audio/audio-metadata-roundtrip.test.ts b/server/src/modules/file-write/formats/audio/audio-metadata-roundtrip.test.ts
index de854e488..5cc190e92 100644
--- a/server/src/modules/file-write/formats/audio/audio-metadata-roundtrip.test.ts
+++ b/server/src/modules/file-write/formats/audio/audio-metadata-roundtrip.test.ts
@@ -106,6 +106,23 @@ describe('audio metadata round-trip', () => {
     expect(extracted.authors).toEqual([{ name: 'Author One', sortName: null }]);
   });
 
+  it('preserves MP3 chapter boundaries across repeated metadata writes', async () => {
+    const filePath = join(tempDir, 'chaptered.mp3');
+    await generateChapteredMp3Fixture(filePath);
+    const chaptersBefore = await probeChapters(filePath);
+    const writer = new Mp3AudioFormatWriter(new AudioMetadataEmbedder({ ffmpegPath, ffprobePath }));
+
+    expect(chaptersBefore).toEqual([
+      { title: 'One', startMs: 0, endMs: 1_500 },
+      { title: 'Two', startMs: 1_500, endMs: 3_000 },
+    ]);
+
+    for (const title of ['First write', 'Second write']) {
+      await writer.write(filePath, { title }, { dryRun: false, fieldMask: new Set(['title']) });
+      expect(await probeChapters(filePath)).toEqual(chaptersBefore);
+    }
+  });
+
   it.each([
     ['m4b', M4bAudioFormatWriter],
     ['m4a', M4aAudioFormatWriter],
@@ -511,10 +528,46 @@ describe('audio metadata round-trip', () => {
     ]);
   }
 
+  async function generateChapteredMp3Fixture(filePath: string): Promise<void> {
+    const chaptersPath = join(tempDir, 'mp3-chapters.txt');
+    await writeFile(
+      chaptersPath,
+      ';FFMETADATA1\n[CHAPTER]\nTIMEBASE=1/1000\nSTART=0\nEND=1500\ntitle=One\n[CHAPTER]\nTIMEBASE=1/1000\nSTART=1500\nEND=3000\ntitle=Two\n',
+    );
+    await execFile(ffmpegPath, [
+      '-v',
+      'error',
+      '-y',
+      '-f',
+      'lavfi',
+      '-i',
+      'sine=frequency=1000:duration=3:sample_rate=44100',
+      '-i',
+      chaptersPath,
+      '-map_metadata',
+      '1',
+      '-map_chapters',
+      '1',
+      '-c:a',
+      'libmp3lame',
+      filePath,
+    ]);
+  }
+
   async function probeChapterTitles(filePath: string): Promise<string[]> {
+    return (await probeChapters(filePath)).map((chapter) => chapter.title);
+  }
+
+  async function probeChapters(filePath: string): Promise<Array<{ title: string; startMs: number; endMs: number }>> {
     const { stdout } = await execFile(ffprobePath, ['-v', 'quiet', '-print_format', 'json', '-show_chapters', filePath]);
-    const parsed = JSON.parse(stdout) as { chapters?: Array<{ tags?: { title?: string } }> };
-    return (parsed.chapters ?? []).map((chapter) => chapter.tags?.title ?? '');
+    const parsed = JSON.parse(stdout) as {
+      chapters?: Array<{ start_time: string; end_time: string; tags?: { title?: string } }>;
+    };
+    return (parsed.chapters ?? []).map((chapter) => ({
+      title: chapter.tags?.title ?? '',
+      startMs: Math.round(Number(chapter.start_time) * 1000),
+      endMs: Math.round(Number(chapter.end_time) * 1000),
+    }));
   }
 
   async function extractArt(filePath: string): Promise<string> {