Spread of Islam
Ottoman Islamic standards of toleration allowed for autonomous "nations" ("millets") in the Empire, under their own personal law and under the rule of their own religious leaders. As a result, vast areas of the Balkans remained mostly Christian during the period of Ottoman domination. In fact, the Eastern Orthodox Churches had a higher position in the Ottoman Empire, mainly because the Patriarch resided in Istanbul and was an officer of the Ottoman Empire. In contrast, Roman Catholics, while tolerated, were suspected of loyalty to a foreign power (the Papacy). It is no surprise that the Roman Catholic areas of Bosnia, Kosovo and northern Albania, ended up with more substantial conversions to Islam. The defeat of the Ottomans in 1699 by the Austrians resulted in their loss of Hungary and present-day Croatia. The remaining Muslim converts in both elected to leave "lands of unbelief" and moved to territory still under the Ottomans. Around this point in time, new European ideas of romantic nationalism started to seep into the Empire, and provided the intellectual foundation for new nationalistic ideologies and the reinforcement of the self-image of many Christian groups as subjugated peoples.
As a rule, the Ottomans did not require followers of Greek Orthodoxy to become Muslims, although many did so in order to avert the socioeconomic hardships of Ottoman rule 
One by one, the Balkan nationalities asserted their independence from the Empire, and frequently the presence of members of the same ethnicity who had converted to Islam presented a problem from the point of view of the now dominant new national ideology, which narrowly defined the nation as members of the local dominant Orthodox Christian denomination. Some Muslims in the Balkans chose to leave, while many others were forcefully expelled to what was left of the Ottoman Empire. This demographic transition can be illustrated by the decrease in the number of mosques in Belgrade, from over 70 in 1750 (before Serbian independence in 1815), to only three in 1850.
Ottoman Crete
One result of the Ottoman conquest was that a sizeable proportion of the population gradually converted to Islam, with its tax and other civic advantages in the Ottoman system. Contemporary estimates vary, but on the eve of the Greek War of Independence as much as 45% of the population of the island may have been Muslim. A small number of these were crypto-Christians who converted back to Christianity; others fled Crete because of the unrest. By the last Ottoman census in 1881, Christians were 76% of the population, and Muslims (usually called "Turks" regardless of language, culture, and ancestry) only 24%, but Muslims were over 60% in the three large towns on the north coast and Monofatsi. Christians were 93% of the population in 1923 of the districts of Crete. The remaining Muslims were transferred to Turkey in the population exchange by religion between Greece and Turkey.