After Crete fell to the Turks in September 1669, the Venetian club ceased to serve its original function. Having no use for such establishments, the Turks used it to house the Defterdar's supreme Treasury of Crete, which also used the adjacent Armeria.

The building housed the Secretary of the Sublime Porte, who was a Christian civil servant charged with representing non-Muslim subjects and transacting their affairs with the Turkish authorities.

We can be sure that no major alterations were made to the Loggia under Ottoman rule (1669-1898). The only modification involved bricking up the arches or fitting them with wooden doors.