Jews were not the target of the Inquisition. The Inquisition was, in a sense, internal quality control for the Church. It was only interested in Catholics. They paid special interest to converts from Islam and Judaism, in part because a stated goal of the Spanish monarchs was a pure Catholic society, and syncretism and false conversion threatened that society. Jews, however, like Muslims, were outside the Inquisition's jurisdiction.

One of the reasons for the spanish inquisition was to ensure that the converts from Judaism and Islam remained true to Orthodox Christianity. Much more so after it was decreed in 1492 that jews and muslims had the choice between converting, or leaving Spain.