A plaque at the entrance of Agios Nikolaos gives its history. The church was originally part of the thirteenth century monastery of Agios Nikolaos (the cloister is still evident on the north side of the church). The church of Agios Nikolaos in Chania was considered one of the most important in the city during Venetian times. It was wide and elegant with large pointed arches inside. The church was converted to the Sultan Ibrahim Mosque during the Turkish occupation. Today, although drastically renovated, the external walls and a long domed area separated in small sections on the north side of the church survive.

The minaret of the Ibrahim Mosque stands beside the church of Agios Nikolaos and is in desperate need of renovation. During a mild earthquake in May 1994 it was feared that the minaret would collapse.