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.
Protestantism and Islam
The Sultan of the Ottoman Empire was known for his tolerance of the Christian and Jewish faiths within his dominions, whereas the King of Spain did not tolerate the Protestant faith. The Ottoman Empire was indeed known at that time for its religious tolerance. Various religious refugees, such as the Huguenots, some Anglicans, Quakers, Anabaptists or even Jesuits or Capuchins were able to find refuge at Istanbul and in the Ottoman Empire, where they were given right of residence and worship. Further, the Ottomans supported the Calvinists in Transylvania and Hungary but also in France. The contemporary French thinker Jean Bodin wrote:
Martin Luther, in his 1528 pamphlet, "On War against the Turk", calls for the Germans to resist the Ottoman invasion of Europe, as the catastrophic Siege of Vienna was lurking, but expressed views of Islam which, compared to his aggressive speech against Catholicism (and later Judaísm), are relatively mild. Concerned with his personal preaching on divine atonement and Christian justification, he extensively criticized the principles of Islam as "utterly despicable and blasphemous", considering Qu'ran as void of any tract of divine truth. For Luther, it was mandatory to let the Qu'ran "speak for itself" as means to show what the Christian Religion saw as a draft from prophetic and apostolic teaching, therefore allowing a proper Christian response. His knowledge on the subject was based on a medieval polemicist version of the Qu'ran made by Riccoldo da Monte di Croce, which was the European scholarly reference of the subject. Luther was writing his own translation of Riccoldo's "Refutation of the Koran" in 1542 when wrote a letter to Basle's city council to relieve the ban on Theodore Bibliander's translation of the Qu'ran into Latin. Mostly due to his letter, Bibliander's translation was finally allowed and eventually published in 1543, with a preface made by Martin Luther himself. His own translation of Riccoldo was also the first version of Koranic material in the German Language. With access to the actual Qu'ran, Luther saw some of Ricoldo's critics as actually exaggerated, but nevertheless agreeing with virtually all of them. .