On 22 February 1549, Pope Paul III named Carafa Archbishop of Naples, but Emperor Charles V prevented him from taking possession of that see until July 1551. Carafa, who was active in Rome as one of the six cardinals of the Roman Inquisition (1542–1555), appointed Rebiba as his vicar to administer the diocese on his behalf. Rebiba was also promoted from auxiliary and on 12 October 1551 made Bishop of Motula, a see in the Kingdom of Naples. With the full support of the head of the Inquisition in Rome, Rebiba introduced the Roman Inquisition into Naples and was granted the office of Commissary of the Roman Inquisition.