diff --git a/fftools/ffmpeg.c b/fftools/ffmpeg.c
index 9b6bb3d759..8ab8aee711 100644
--- a/fftools/ffmpeg.c
+++ b/fftools/ffmpeg.c
@@ -3478,12 +3478,6 @@ static int need_output(void)
 
         if (ost->finished || of_finished(of))
             continue;
-        if (ost->frame_number >= ost->max_frames) {
-            int j;
-            for (j = 0; j < of->ctx->nb_streams; j++)
-                close_output_stream(output_streams[of->ost_index + j]);
-            continue;
-        }
 
         return 1;
     }
diff --git a/fftools/ffmpeg_mux.c b/fftools/ffmpeg_mux.c
index 641bdb98b0..56444770bf 100644
--- a/fftools/ffmpeg_mux.c
+++ b/fftools/ffmpeg_mux.c
@@ -237,19 +237,11 @@ void of_submit_packet(OutputFile *of, AVPacket *pkt, OutputStream *ost)
 
     if (pkt) {
         /*
-         * Audio encoders may split the packets --  #frames in != #packets out.
-         * But there is no reordering, so we can limit the number of output packets
-         * by simply dropping them here.
          * Counting encoded video frames needs to be done separately because of
          * reordering, see do_video_out().
          */
-        if (!(st->codecpar->codec_type == AVMEDIA_TYPE_VIDEO && ost->encoding_needed)) {
-            if (ost->frame_number >= ost->max_frames) {
-                av_packet_unref(pkt);
-                return;
-            }
+        if (!(st->codecpar->codec_type == AVMEDIA_TYPE_VIDEO && ost->encoding_needed))
             ost->frame_number++;
-        }
     }
 
     if (of->mux->header_written) {
diff --git a/fftools/ffmpeg_opt.c b/fftools/ffmpeg_opt.c
index 4281644cfc..f7b5ce347b 100644
--- a/fftools/ffmpeg_opt.c
+++ b/fftools/ffmpeg_opt.c
@@ -2390,6 +2390,7 @@ static int init_complex_filters(void)
 static int setup_sync_queues(OutputFile *of, AVFormatContext *oc, int64_t buf_size_us)
 {
     int nb_av_enc = 0, nb_interleaved = 0;
+    int limit_frames = 0, limit_frames_av_enc = 0;
 
 #define IS_AV_ENC(ost, type)  \
     (ost->encoding_needed && (type == AVMEDIA_TYPE_VIDEO || type == AVMEDIA_TYPE_AUDIO))
@@ -2404,14 +2405,19 @@ static int setup_sync_queues(OutputFile *of, AVFormatContext *oc, int64_t buf_si
 
         nb_interleaved += IS_INTERLEAVED(type);
         nb_av_enc      += IS_AV_ENC(ost, type);
+
+        limit_frames        |=  ost->max_frames < INT64_MAX;
+        limit_frames_av_enc |= (ost->max_frames < INT64_MAX) && IS_AV_ENC(ost, type);
     }
 
-    if (!(nb_interleaved > 1 && of->shortest))
+    if (!((nb_interleaved > 1 && of->shortest) ||
+          (nb_interleaved > 0 && limit_frames)))
         return 0;
 
-    /* if we have more than one encoded audio/video streams, then we
+    /* if we have more than one encoded audio/video streams, or at least
+     * one encoded audio/video stream is frame-limited, then we
      * synchronize them before encoding */
-    if (nb_av_enc > 1) {
+    if ((of->shortest && nb_av_enc > 1) || limit_frames_av_enc) {
         of->sq_encode = sq_alloc(SYNC_QUEUE_FRAMES, buf_size_us);
         if (!of->sq_encode)
             return AVERROR(ENOMEM);
@@ -2423,13 +2429,17 @@ static int setup_sync_queues(OutputFile *of, AVFormatContext *oc, int64_t buf_si
             if (!IS_AV_ENC(ost, type))
                 continue;
 
-            ost->sq_idx_encode = sq_add_stream(of->sq_encode);
+            ost->sq_idx_encode = sq_add_stream(of->sq_encode,
+                                               of->shortest || ost->max_frames < INT64_MAX);
             if (ost->sq_idx_encode < 0)
                 return ost->sq_idx_encode;
 
             ost->sq_frame = av_frame_alloc();
             if (!ost->sq_frame)
                 return AVERROR(ENOMEM);
+
+            if (ost->max_frames != INT64_MAX)
+                sq_limit_frames(of->sq_encode, ost->sq_idx_encode, ost->max_frames);
         }
     }
 
@@ -2447,9 +2457,13 @@ static int setup_sync_queues(OutputFile *of, AVFormatContext *oc, int64_t buf_si
             if (!IS_INTERLEAVED(type))
                 continue;
 
-            ost->sq_idx_mux = sq_add_stream(of->sq_mux);
+            ost->sq_idx_mux = sq_add_stream(of->sq_mux,
+                                            of->shortest || ost->max_frames < INT64_MAX);
             if (ost->sq_idx_mux < 0)
                 return ost->sq_idx_mux;
+
+            if (ost->max_frames != INT64_MAX)
+                sq_limit_frames(of->sq_mux, ost->sq_idx_mux, ost->max_frames);
         }
     }
 
diff --git a/fftools/sync_queue.c b/fftools/sync_queue.c
index ab654ca790..3143d12cf1 100644
--- a/fftools/sync_queue.c
+++ b/fftools/sync_queue.c
@@ -34,8 +34,12 @@ typedef struct SyncQueueStream {
 
     /* stream head: largest timestamp seen */
     int64_t          head_ts;
+    int              limiting;
     /* no more frames will be sent for this stream */
     int              finished;
+
+    uint64_t         frames_sent;
+    uint64_t         frames_max;
 } SyncQueueStream;
 
 struct SyncQueue {
@@ -86,7 +90,7 @@ static void finish_stream(SyncQueue *sq, unsigned int stream_idx)
 
     st->finished = 1;
 
-    if (st->head_ts != AV_NOPTS_VALUE) {
+    if (st->limiting && st->head_ts != AV_NOPTS_VALUE) {
         /* check if this stream is the new finished head */
         if (sq->head_finished_stream < 0 ||
             av_compare_ts(st->head_ts, st->tb,
@@ -121,7 +125,7 @@ static void queue_head_update(SyncQueue *sq)
          * the queue head */
         for (unsigned int i = 0; i < sq->nb_streams; i++) {
             SyncQueueStream *st = &sq->streams[i];
-            if (st->head_ts == AV_NOPTS_VALUE)
+            if (st->limiting && st->head_ts == AV_NOPTS_VALUE)
                 return;
         }
 
@@ -132,7 +136,7 @@ static void queue_head_update(SyncQueue *sq)
     for (unsigned int i = 0; i < sq->nb_streams; i++) {
         SyncQueueStream *st_head  = &sq->streams[sq->head_stream];
         SyncQueueStream *st_other = &sq->streams[i];
-        if (st_other->head_ts != AV_NOPTS_VALUE &&
+        if (st_other->limiting && st_other->head_ts != AV_NOPTS_VALUE &&
             av_compare_ts(st_other->head_ts, st_other->tb,
                           st_head->head_ts,  st_head->tb) < 0)
             sq->head_stream = i;
@@ -159,7 +163,8 @@ static void stream_update_ts(SyncQueue *sq, unsigned int stream_idx, int64_t ts)
         finish_stream(sq, stream_idx);
 
     /* update the overall head timestamp if it could have changed */
-    if (sq->head_stream < 0 || sq->head_stream == stream_idx)
+    if (st->limiting &&
+        (sq->head_stream < 0 || sq->head_stream == stream_idx))
         queue_head_update(sq);
 }
 
@@ -262,6 +267,10 @@ int sq_send(SyncQueue *sq, unsigned int stream_idx, SyncQueueFrame frame)
 
     stream_update_ts(sq, stream_idx, ts);
 
+    st->frames_sent++;
+    if (st->frames_sent >= st->frames_max)
+        finish_stream(sq, stream_idx);
+
     return 0;
 }
 
@@ -339,7 +348,7 @@ int sq_receive(SyncQueue *sq, int stream_idx, SyncQueueFrame frame)
     return ret;
 }
 
-int sq_add_stream(SyncQueue *sq)
+int sq_add_stream(SyncQueue *sq, int limiting)
 {
     SyncQueueStream *tmp, *st;
 
@@ -360,6 +369,8 @@ int sq_add_stream(SyncQueue *sq)
      * streams forever; cf. overflow_heartbeat() */
     st->tb      = (AVRational){ 1, 1 };
     st->head_ts = AV_NOPTS_VALUE;
+    st->frames_max = UINT64_MAX;
+    st->limiting   = limiting;
 
     return sq->nb_streams++;
 }
@@ -379,6 +390,18 @@ void sq_set_tb(SyncQueue *sq, unsigned int stream_idx, AVRational tb)
     st->tb = tb;
 }
 
+void sq_limit_frames(SyncQueue *sq, unsigned int stream_idx, uint64_t frames)
+{
+    SyncQueueStream *st;
+
+    av_assert0(stream_idx < sq->nb_streams);
+    st = &sq->streams[stream_idx];
+
+    st->frames_max = frames;
+    if (st->frames_sent >= st->frames_max)
+        finish_stream(sq, stream_idx);
+}
+
 SyncQueue *sq_alloc(enum SyncQueueType type, int64_t buf_size_us)
 {
     SyncQueue *sq = av_mallocz(sizeof(*sq));
diff --git a/fftools/sync_queue.h b/fftools/sync_queue.h
index e08780b7bf..3f823ff0d9 100644
--- a/fftools/sync_queue.h
+++ b/fftools/sync_queue.h
@@ -51,11 +51,13 @@ void       sq_free(SyncQueue **sq);
 /**
  * Add a new stream to the sync queue.
  *
+ * @param limiting whether the stream is limiting, i.e. no other stream can be
+ *                 longer than this one
  * @return
  * - a non-negative stream index on success
  * - a negative error code on error
  */
-int sq_add_stream(SyncQueue *sq);
+int sq_add_stream(SyncQueue *sq, int limiting);
 
 /**
  * Set the timebase for the stream with index stream_idx. Should be called
@@ -63,6 +65,13 @@ int sq_add_stream(SyncQueue *sq);
  */
 void sq_set_tb(SyncQueue *sq, unsigned int stream_idx, AVRational tb);
 
+/**
+ * Limit the number of output frames for stream with index stream_idx
+ * to max_frames.
+ */
+void sq_limit_frames(SyncQueue *sq, unsigned int stream_idx,
+                     uint64_t max_frames);
+
 /**
  * Submit a frame for the stream with index stream_idx.
  *
diff --git a/tests/ref/fate/matroska-flac-extradata-update b/tests/ref/fate/matroska-flac-extradata-update
index e8812f51b5..d5814925f5 100644
--- a/tests/ref/fate/matroska-flac-extradata-update
+++ b/tests/ref/fate/matroska-flac-extradata-update
@@ -1,8 +1,8 @@
-732446e97bae29037ff0cd9963d4ac08 *tests/data/fate/matroska-flac-extradata-update.matroska
-1987 tests/data/fate/matroska-flac-extradata-update.matroska
-#extradata 0:       34, 0x7acb09e7
-#extradata 1:       34, 0x7acb09e7
-#extradata 2:       34, 0x443402dd
+28bc0ded5dc520d955caf29db80d35da *tests/data/fate/matroska-flac-extradata-update.matroska
+1795 tests/data/fate/matroska-flac-extradata-update.matroska
+#extradata 0:       34, 0x93650c81
+#extradata 1:       34, 0x93650c81
+#extradata 2:       34, 0x93650c81
 #tb 0: 1/1000
 #media_type 0: audio
 #codec_id 0: flac
@@ -42,9 +42,3 @@
 0,        672,        672,       96,       26, 0x50dd042e
 1,        672,        672,       96,       26, 0x50dd042e
 2,        672,        672,       96,       26, 0x50dd042e
-0,        768,        768,       96,       26, 0x53de0499
-1,        768,        768,       96,       26, 0x53de0499
-0,        864,        864,       96,       26, 0x53df04b4
-1,        864,        864,       96,       26, 0x53df04b4
-0,        960,        960,       42,       26, 0x5740044b
-1,        960,        960,       42,       26, 0x5740044b
diff --git a/tests/ref/fate/mkv-1242 b/tests/ref/fate/mkv-1242
index e025701093..1d1a227832 100644
--- a/tests/ref/fate/mkv-1242
+++ b/tests/ref/fate/mkv-1242
@@ -42,6 +42,3 @@
 1,        383,        383,       21,      325, 0xcd7a9fd6
 1,        404,        404,       22,      359, 0x6edeb91c
 1,        426,        426,       21,      333, 0xb8999fb7
-1,        447,        447,       21,      317, 0xf2589e1a
-1,        468,        468,       21,      319, 0x82ed9572
-1,        489,        489,       22,      473, 0xea54e696