The katholikon (principal monastery church) in the Monastery of St. Francis was the grandest of its kind in Chandax. Owned by the Franciscan order, it stood on the site of the Archaeological Museum, in the northeast corner of what is now Eleftherias Square.

In Ottoman times the church was converted into a mosque dedicated to Sultan Mohammed the Conqueror and named the Hukniar (Imperial) Mosque. The only remnant to survive into the early 20th century was the sacristy adjoining the church, which was demolished during building work on the new Heraklion museum.

The Franciscan friary stood on the site now occupied by the Archaeological Museum. Following the conquest of Chandax in 1669 it was converted into a mosque, 1900 - 1905 (G. Gerola, Vikelaia Municipal Library, Heraklion)
The sacristy forming part of the Church of San Francesco, following conversion into a mosque, - (Heraklion)
The Champs de Mars, with San Francesco in the background to the right, 1900 - 1905 (Vikelaia Municipal Library, Heraklion)