(Expanding on the solution from oldmankit over at Ubuntu Forums)

1. Install bchunk and flac:

   sudo apt install bchunk flac
   

2. Use bchunk to convert the .bin to WAV files:

   bchunk -w image.bin image.cue track
   

3. Use flac to compress the WAV files:

   for f in track*.wav; do flac $f; done
   

Naming and tagging the FLAC files is subject for another question, but cuetools (particularly the cueprint command) may be of help there.

I’ve downloaded the .bin, .cue and .cdt files of an audio CD (freely available), but I’d prefer to have the audio in FLAC format on my computer. How do I convert the audio tracks of the .bin file to FLAC files without losing quality?

I’m using Ubuntu 16.04.