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.
Composite monarchy
The Ottoman Empire’s most striking difference with other composite monarchies in Europe was that it allowed religious freedom to a much greater extent than the Europeans did. Religious warfare proliferated in the early modern period (especially in the 16th and 17th centuries). The Ottomans did not require that their subjects adhere to the religion of the monarch, a requirement that usually was a major part of composite kingdoms. The Ottoman Empire was extremely diverse and there were relatively few restrictions on activity of minority groups. Christians, Muslims, Jews, Turks, Greeks, Hungarians, Arabs, Armenians, Kurds, guildsmen, bureaucrats and slaves were free to work and live throughout the empire. This level of religious freedom was largely alien to the rest of Europe during the early modern period. The Spanish Inquisition and the ghettos in Italy were examples of the religious restriction and intolerance within non-Ottoman Europe.