In 1669, following the fall of Candia, Ottoman authorities, officials and ordinary soldiers settled in the city without delay. As the Muslim population increased, there was an urgent need for places of worship in Kandiye. Mosques were required not only to serve religious needs but also symbolised the transformation of a formerly Christian city into an Ottoman one. To meet this need, Orthodox and Catholic churches were converted into Muslim mosques.

Because of its commanding position on a hill at the eastern edge of the city and its large size, the church of St Francis Church was converted into an imperial mosque dedicated to the reigning Sultan Mehmed IV. The Dominican church of St Peter of the Dominicans, which dominated the city’s seafront, became the Sultan Ibrahim Mosque, transferred from the outwork of Fortezza, during whose reign the Cretan War had begun. The Augustinian church of Church of the Saviour was converted into a mosque of the Valide Sultan, while St Titus Church became a mosque dedicated to the conqueror of the city, Fazıl Ahmed Köprülü (Vezir Camii). The neighbouring St Mark’s Church was converted into a mosque associated with Defterdar Ahmed Pasha, the empire’s chief financial official who accompanied the Grand Vizier to Crete. Additional mosques were founded in the city centre by leading generals and high-ranking officials of the conquering army.

The Ottomans interventions to Christian monuments were limited to those necessary for conversion into mosques. These included the construction of a mihrab, a small niche indicating the direction of Mecca, the installation of a minbar (pulpit) to the right of the mihrab, the covering of wall paintings, and the erection of a minaret, usually on the site of the former bell tower. Many mosques were accompanied by schools, religious colleges, public baths, fountains and poorhouses. Alongside the large mosques, smaller neighbourhood prayer halls (mescit) also existed. Only two entirely new mosques were built from the ground up: the Mosque of the Conquest (Fethiye Camii) and the New Mosque (Yeni Camii), completed in 1700.

A large number of small churches—such as Panagia Phaneromeni—were converted into neighbourhood prayer halls (mescit) or into monasteries known as tekkes, founded by Muslim religious figures. These tekkes were established by various dervish orders, whose activities played a significant role in the Islamisation of the local population. The most important was the tekke of Horasanli Ali Baba, belonging to the Bektashi order, which survives in the neighbourhood of Nea Alatsata. Also well known were the tekke of Ali Dede near the western gate, Karanlık Kapı (Bethlehem Gate), and the tekke of the Üç Er known as Otsleria.