They tended to be a mix of Muslims and non Muslims. A large number of the Muslims in the Balkans were in said cities, either being converts, settlers or administrators. The cities themselves were more Turkish Muslim heavy, due to the whole administration aspect but there were many non Turkish Muslims as well. As for non Muslims, there were significant amounts of Armenians throughout the empire and depending on the exact city you would get the "native" population as well as people's from neighboring countries. One example would be Bulgarians in Thessaloniki. That city in particular was interesting, as it had a large Jewish population. Overall they tended to be quite cosmopolitan, but It is a vague question to ask

There is good coverage of this in Greene, Molly, a Shared World: Christians and Muslims in the Early Modern Mediterranean (New Jersey, 2000).

Greene uses the example of Candia to juxtapose the Venetian and Ottoman Rule of the city and island. The blend of Catholicism and Orthodoxy that mingled so well was emphatically changed under Ottoman Rule. It's a decent enough comparison if you want to look at that. It is primarily religious but it does show the cultural composition of a conquered city.