diff --git a/libavformat/matroskadec.c b/libavformat/matroskadec.c
index 95e49cbe7f..5789e35949 100644
--- a/libavformat/matroskadec.c
+++ b/libavformat/matroskadec.c
@@ -2082,7 +2082,7 @@ static int matroska_parse_flac(AVFormatContext *s,
                     av_log(s, AV_LOG_WARNING,
                            "Invalid value of WAVEFORMATEXTENSIBLE_CHANNEL_MASK\n");
                 } else
-                    st->codecpar->channel_layout = mask;
+                    av_channel_layout_from_mask(&st->codecpar->ch_layout, mask);
             }
             av_dict_free(&dict);
         }
@@ -2945,7 +2945,11 @@ static int matroska_parse_tracks(AVFormatContext *s)
             st->codecpar->codec_type  = AVMEDIA_TYPE_AUDIO;
             st->codecpar->codec_tag   = fourcc;
             st->codecpar->sample_rate = track->audio.out_samplerate;
-            st->codecpar->channels    = track->audio.channels;
+            // channel layout may be already set by codec private checks above
+            if (st->codecpar->ch_layout.order == AV_CHANNEL_ORDER_NATIVE &&
+                !st->codecpar->ch_layout.u.mask)
+                st->codecpar->ch_layout.order = AV_CHANNEL_ORDER_UNSPEC;
+            st->codecpar->ch_layout.nb_channels = track->audio.channels;
             if (!st->codecpar->bits_per_coded_sample)
                 st->codecpar->bits_per_coded_sample = track->audio.bitdepth;
             if (st->codecpar->codec_id == AV_CODEC_ID_MP3 ||
diff --git a/libavformat/matroskaenc.c b/libavformat/matroskaenc.c
index 38d9485288..b39157538c 100644
--- a/libavformat/matroskaenc.c
+++ b/libavformat/matroskaenc.c
@@ -1009,9 +1009,9 @@ static int put_wv_codecpriv(AVIOContext *pb, const AVCodecParameters *par)
 static int put_flac_codecpriv(AVFormatContext *s, AVIOContext *pb,
                               const AVCodecParameters *par)
 {
-    int write_comment = (par->channel_layout &&
-                         !(par->channel_layout & ~0x3ffffULL) &&
-                         !ff_flac_is_native_layout(par->channel_layout));
+    int write_comment = (par->ch_layout.order == AV_CHANNEL_ORDER_NATIVE &&
+                         !(par->ch_layout.u.mask & ~0x3ffffULL) &&
+                         !ff_flac_is_native_layout(par->ch_layout.u.mask));
     int ret = ff_flac_write_header(pb, par->extradata, par->extradata_size,
                                    !write_comment);
 
@@ -1025,7 +1025,7 @@ static int put_flac_codecpriv(AVFormatContext *s, AVIOContext *pb,
         uint8_t buf[32];
         int64_t len;
 
-        snprintf(buf, sizeof(buf), "0x%"PRIx64, par->channel_layout);
+        snprintf(buf, sizeof(buf), "0x%"PRIx64, par->ch_layout.u.mask);
         av_dict_set(&dict, "WAVEFORMATEXTENSIBLE_CHANNEL_MASK", buf, 0);
 
         len = ff_vorbiscomment_length(dict, vendor, NULL, 0);
@@ -1769,7 +1769,7 @@ static int mkv_write_track(AVFormatContext *s, MatroskaMuxContext *mkv,
             put_ebml_string(pb, MATROSKA_ID_CODECID, "A_MS/ACM");
 
         subinfo = start_ebml_master(pb, MATROSKA_ID_TRACKAUDIO, 6 + 4 * 9);
-        put_ebml_uint  (pb, MATROSKA_ID_AUDIOCHANNELS    , par->channels);
+        put_ebml_uint(pb, MATROSKA_ID_AUDIOCHANNELS, par->ch_layout.nb_channels);
 
         track->sample_rate_offset = avio_tell(pb);
         put_ebml_float (pb, MATROSKA_ID_AUDIOSAMPLINGFREQ, sample_rate);