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.
Islam in Albania (1800–1912)
At the beginning of the 19th century Albanians were divided into three religious groups. Catholic Albanians who had some Albanian ethno-linguistic expression in schooling and church due to Austro-Hungarian protection and Italian clerical patronage. Orthodox Albanians under the Patriarchate of Constantinople had liturgy and schooling in Greek and toward the late Ottoman period mainly identified with Greek national aspirations. While Muslim Albanians during this period formed around 70% of the overall Balkan Albanian population in the Ottoman Empire with an estimated population of more than a million. With the rise of the Eastern Crisis, Muslim Albanians became torn between loyalties to the Ottoman state and the emerging Albanian nationalist movement. Islam, the Sultan and the Ottoman Empire were traditionally seen as synonymous in belonging to the wider Muslim community. While the Albanian nationalist movement advocated self-determination and strived to achieve socio-political recognition of Albanians as a separate people and language within the state. Between 1839 and 1876, the Ottoman Empire initiated modernising government reforms during the Tanzimat period and the Albanian Ottoman elite opposed them, in particular of having Ottoman officials from other parts of the empire sent to govern Ottoman Albanian areas and the introduction of a new centralised military recruitment system.