Comment by bluGill

Organs are and were tuned all the time. While he didn't have a piano, the organ was tempered in some way.

His well tempered clavier was a plea to give him organs that could play in any key. We don't know what temperament he used (there is plenty of debate), but it is clear he was trying to show how the key in his system changes the sound/mood of the piece - something lost in equal temperament.