The Inquisition did not target Muslims or Jews.
The Inquisition targeted Catholic heretics, include alleged converts (hence, officially Catholic) who didn't actually believe in or practice the faith.
Muslims and Jews who didn't claim to be Catholic were left alone by the Inquisition.
Muslims and Jews were expelled by Ferdinand and Isabella, but that was done by the secular government, not by the church.
I will agree that the Church usaily did a good job of protecting Jews in Europe.