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 Christian population of the empire, owing to their higher educational levels, started to pull ahead of the Muslim majority, leading to much resentment on the part of the latter. In 1861, there were 571 primary and 94 secondary schools for Ottoman Christians with 140,000 pupils in total, a figure that vastly exceeded the number of Muslim children in school at the same time, who were further hindered by the amount of time spent learning Arabic and Islamic theology. Stone further suggested that the Arabic alphabet, which Turkish was written in until 1928, was very ill-suited to reflect the sounds of the Turkish language (which is a Turkic as opposed to Semitic language), which imposed a further difficulty on Turkish children. In turn, the higher educational levels of the Christians allowed them to play a larger role in the economy, with the rise in prominence of groups such as the Sursock family indicative of this shift in influence. In 1911, of the 654 wholesale companies in Istanbul, 528 were owned by ethnic Greeks. In many cases, Christians and also Jews were able to gain protection from European consuls and citizenship, meaning they were protected from Ottoman law and not subject to the same economic regulations as their Muslim comrades.