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.
Christianity in the Ottoman Empire
The state's relationship with the Greek Orthodox Church was mixed, since the Orthodox were not killed, they were in the beginning the vast majority and taxpayers, they were encouraged through bribes and exemptions to convert to Islam. In turn they could not proselytize Muslims. The church's structure was kept intact and largely left alone (but under close control and scrutiny) until the Greek War of Independence of 1821–1831 and, later in the 19th and early 20th centuries, during the rise of the Ottoman constitutional monarchy, which was driven to some extent by nationalistic currents. But the Church was greatly affected by the corruption brought in by the Ottoman system of choosing the Patriarch of Constantinople, and putting up the position of Patriarch for bribes. Other churches, like the Serbian Patriarchate of Peć (1766) and Archbishopric of Ohrid (1767), were dissolved and their dioceses placed under the jurisdiction of the Ecumenical Patriarchate of Constantinople. Churches had to be placed in inconspicuous areas, where the everyday populace would not see them.