Despite the efforts of the Venetians to reinforce the defense of the island, they were not able to protect it from the Turkish threat. The Turks were determined to establish their authority in the Mediterranean, and after a long period of instability, fights, lootings and diplomacy, the occupation of Crete by the Turks finally started in 1645.

In June 1645, Gioushouf Pasha and his army disembarked in Kissamos and Kolympari and attacked the fortress of the Theodorou island.  In June 15 of the same year, the siege of the city of Chania begins and after 57 days of struggles the city is finally surrendered. The whole island of Crete was occupied in 1669, after 25 years of war.

After the occupation of the city, the new conquerors brought back the orthodox Bishop of Kydonia in his ancient Episcopal see, at the temple of Aghioi Anargyroi, in an effort to please the local population.
They also converted old Catholic Churches into Mosques and also constructed new Mosques in the city. They also founded public baths, from which only three are preserved today, as well as public water fountains, usually located next to the Mosques.
Other public buildings were also constructed, such as hospitals, barracks and other military buildings, the Venetian fortress was reinforced and the urban plan was limited within its limits.

With the Turkish occupation, the socio-political conditions change dramatically in the city of Chania. Wealthy Muslim families become the new upper class and feudal lords. The new living conditions are closely connected to the religion and social organization of the conquerors. The city of Chania becomes the headquarters of the Turkish Pasha.

The 1770 revolution led by Daskalogiannis-Vlachos from Sfakia, who was heinously executed (he was flayed alive), as well as the numerous revolutions that followed throughout the 19^th century greatly influenced the socio-political structures of Crete and the developments in administration and culture.

The great 1821 national revolution shattered the relations between the Turkish and the Greek population in Crete and bloody massacres took place in the city of Chania.