diff --git a/youtube_dlc/__init__.py b/youtube_dlc/__init__.py
index d28510467..eeb7b6f74 100644
--- a/youtube_dlc/__init__.py
+++ b/youtube_dlc/__init__.py
@@ -233,11 +233,6 @@ def _real_main(argv=None):
     if opts.extractaudio and not opts.keepvideo and opts.format is None:
         opts.format = 'bestaudio/best'
 
-    # --all-sub automatically sets --write-sub if --write-auto-sub is not given
-    # this was the old behaviour if only --all-sub was given.
-    if opts.allsubtitles and not opts.writeautomaticsub:
-        opts.writesubtitles = True
-
     outtmpl = opts.outtmpl
     if not outtmpl:
         outtmpl = {'default': (
@@ -311,9 +306,17 @@ def _real_main(argv=None):
             'format': opts.convertsubtitles,
         })
     if opts.embedsubtitles:
+        already_have_subtitle = opts.writesubtitles
         postprocessors.append({
             'key': 'FFmpegEmbedSubtitle',
+            'already_have_subtitle': already_have_subtitle
         })
+        if not already_have_subtitle:
+            opts.writesubtitles = True
+    # --all-sub automatically sets --write-sub if --write-auto-sub is not given
+    # this was the old behaviour if only --all-sub was given.
+    if opts.allsubtitles and not opts.writeautomaticsub:
+        opts.writesubtitles = True
     if opts.embedthumbnail:
         already_have_thumbnail = opts.writethumbnail or opts.write_all_thumbnails
         postprocessors.append({
diff --git a/youtube_dlc/postprocessor/ffmpeg.py b/youtube_dlc/postprocessor/ffmpeg.py
index 948c34287..cabe7266e 100644
--- a/youtube_dlc/postprocessor/ffmpeg.py
+++ b/youtube_dlc/postprocessor/ffmpeg.py
@@ -442,6 +442,10 @@ class FFmpegVideoConvertorPP(FFmpegPostProcessor):
 
 
 class FFmpegEmbedSubtitlePP(FFmpegPostProcessor):
+    def __init__(self, downloader=None, already_have_subtitle=False):
+        super(FFmpegEmbedSubtitlePP, self).__init__(downloader)
+        self._already_have_subtitle = already_have_subtitle
+
     def run(self, information):
         if information['ext'] not in ('mp4', 'webm', 'mkv'):
             self.to_screen('Subtitles can only be embedded in mp4, webm or mkv files')
@@ -501,7 +505,8 @@ class FFmpegEmbedSubtitlePP(FFmpegPostProcessor):
         os.remove(encodeFilename(filename))
         os.rename(encodeFilename(temp_filename), encodeFilename(filename))
 
-        return sub_filenames, information
+        files_to_delete = [] if self._already_have_subtitle else sub_filenames
+        return files_to_delete, information
 
 
 class FFmpegMetadataPP(FFmpegPostProcessor):