After the fall of Crete to the Turks in September 1669, the Armeria continued to be used mainly as a store for captured weapons, and was known as the Top-hane (Kebir Top-hane), a term which has survived up to the present day. We can be certain that under Ottoman rule (1669-1898) the Turks made a number of changes to the building, bricking up the doors to the armoury and rebuilding the north side in an inelegant, unadorned fashion, most probably after it collapsed in the 1865 earthquake. According to an account by Nael Vei Afentakis, the armoury wall was built by his father between 1855 and 1860.

A Turkish document dating to 1719 makes mention of a decree by Defterdar Mehmet Pasha, ordering that the Cephane be used to store 96,496 piasters, which amount had been collected as tithes to pay the janissaries.