diff --git a/yt_dlp/postprocessor/ffmpeg.py b/yt_dlp/postprocessor/ffmpeg.py
index 59a49aa57..a4c457617 100644
--- a/yt_dlp/postprocessor/ffmpeg.py
+++ b/yt_dlp/postprocessor/ffmpeg.py
@@ -9,6 +9,7 @@
 import time
 
 from .common import PostProcessor
+from .. import webvtt
 from ..compat import imghdr
 from ..utils import (
     MEDIA_EXTENSIONS,
@@ -618,6 +619,7 @@ def run(self, info):
         sub_langs, sub_names, sub_filenames = [], [], []
         webm_vtt_warn = False
         mp4_ass_warn = False
+        files_to_delete = []
 
         for lang, sub_info in subtitles.items():
             if not os.path.exists(sub_info.get('filepath', '')):
@@ -626,14 +628,41 @@ def run(self, info):
             sub_ext = sub_info['ext']
             if sub_ext == 'json':
                 self.report_warning('JSON subtitles cannot be embedded')
-            elif ext != 'webm' or (ext == 'webm' and sub_ext == 'vtt'):
+            elif ext in ('mkv', 'webm') and sub_ext == 'vtt':
+                # This is a workaround for ffmpeg bug https://trac.ffmpeg.org/ticket/11493
+                # If the WebVTT contains empty text cues, it'll corrupt remuxed Matroska files, dropping frames
                 sub_langs.append(lang)
                 sub_names.append(sub_info.get('name'))
-                sub_filenames.append(sub_info['filepath'])
-            else:
-                if not webm_vtt_warn and ext == 'webm' and sub_ext != 'vtt':
+                original_file = sub_info['filepath']
+                if not self._already_have_subtitle:
+                    files_to_delete.append(original_file)
+
+                with open(original_file, 'rb') as f:
+                    vtt_bytes = f.read()
+                blocks = list(webvtt.parse_fragment(vtt_bytes))
+
+                nonempty_blocks = [block for block in blocks if not isinstance(block, webvtt.CueBlock) or block.text.strip() != '']
+                if len(blocks) != len(nonempty_blocks):
+                    self.report_warning(f'Filtering WebVTT for {lang} subtitle due to ffmpeg bug #11493')
+                    temp_file = prepend_extension(original_file, 'filtered')
+                    with open(temp_file, 'w', encoding='utf-8', newline='\n') as f:
+                        for block in nonempty_blocks:
+                            block.write_into(f)
+                    files_to_delete.append(temp_file)
+                    sub_filenames.append(temp_file)
+                else:
+                    sub_filenames.append(original_file)
+            elif ext == 'webm':
+                if not webm_vtt_warn:
                     webm_vtt_warn = True
                     self.report_warning('Only WebVTT subtitles can be embedded in webm files')
+            else:
+                sub_langs.append(lang)
+                sub_names.append(sub_info.get('name'))
+                filepath = sub_info['filepath']
+                sub_filenames.append(filepath)
+                if not self._already_have_subtitle:
+                    files_to_delete.append(filepath)
             if not mp4_ass_warn and ext == 'mp4' and sub_ext == 'ass':
                 mp4_ass_warn = True
                 self.report_warning('ASS subtitles cannot be properly embedded in mp4 files; expect issues')
@@ -662,7 +691,6 @@ def run(self, info):
         self.run_ffmpeg_multiple_files(input_files, temp_filename, opts)
         os.replace(temp_filename, filename)
 
-        files_to_delete = [] if self._already_have_subtitle else sub_filenames
         return files_to_delete, info