Throughout the period of Venetian rule, distinguished political leaders and prelates from Candia were buried at the church, both in the interior and by the outside walls. In Volume II of his monumental work "Monumenti Veneti nell isola di Creta", G. Gerola mentions that it was the burial place of Dukes of Crete Markos Grandonikos (1331), Ioannis Morosini (1338), Marinos Grimani (1348) and Philippos Dorio (1357).

At the very beginning of Turkish rule Ss. Peter and Paul was converted into a mosque dedicated to the memory of Sultan Ibrahim, and a minaret was added to the southwest corner.

Other features dating to the Ottoman period, uncovered during restoration work, were the mihrab (prayer niche), pebbled floors and a clay furnace.