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 Empire
The Ottoman legal system accepted the religious law over its subjects. At the same time the "Qanun" (or "Kanun"), a secular legal system, co-existed with religious law or Sharia. The Ottoman Empire was always organized around a system of local jurisprudence. Legal administration in the Ottoman Empire was part of a larger scheme of balancing central and local authority. Ottoman power revolved crucially around the administration of the rights to land, which gave a space for the local authority to develop the needs of the local millet. The jurisdictional complexity of the Ottoman Empire was aimed to permit the integration of culturally and religiously different groups. The Ottoman system had three court systems: one for Muslims, one for non-Muslims, involving appointed Jews and Christians ruling over their respective religious communities, and the "trade court". The entire system was regulated from above by means of the administrative "Qanun", i.e. laws, a system based upon the Turkic "Yassa" and "Töre", which were developed in the pre-Islamic era.