Like Torquemada, Deza had a particular dislike of conversos – Jews or Muslims who had converted to Christianity but who were often accused of secretly retaining their original faith.

Like Torquemada, Deza was accused of being overzealous in his work, and of showing excessive cruelty – his reputation was sufficient that in 1507, the Pope was forced to publicly request moderation.

Deza himself was later accused of secretly practising Judaism, a charge mainly based on the fact that he himself had Jewish blood on his mother's side.

Lucero intensely disliked the "false converted", and in 1500 handled papers sent to Pope Julius II on the Archbishop of Granada's (Hernando de Talavera) Jewish ancestry.

Lucero, the Inquisitor of Córdoba, was more hated than Deza, and in late 1506, had narrowly escaped with his life when an angry mob stormed the Inquisition's base in Cordoba and freed all its prisoners.

It is likely that Diego de Deza could have returned to his inquisitorial office, because it is known that he was named Archbishop of Toledo (and thus Primate of Spain), but was not able to take up the position due to illness.

His tomb in his College of Santo Tomas was opened by Napoleonic troops in 1810 with the aim of stealing his rings, collars and golden paraphernalia.