Assuming we have video in 0:0 and only one audio stream in 0:1: ffmpeg -i ${FILEIN} -filter_complex "[0:1][0:1]amerge,channelmap=channel_layout=stereo[st]" -map 0:0 -map "[st]" -c:v copy -c:a pcm_s16le -ar 48k ${FILEOUT}