Close-knit national churches, like the Syrian and Coptic ones did not become subject to separate political ends and remained loyal to the Empire. In contrast, religious institutions submitted to regional and local patriotism when regional feudal lords managed to temporarily break politically ties with the imperial center. This was evidenced by the creation of the autonomous Bulgarian and Serbian churches in 870 and 1219 respectively.

As the empire gradually split into two parts, one West and one East, the church followed according to political divisions and geopolitical interests. As a result, the Church in the east became the Orthodox church, and the Church in the west, became the Catholic church. Both churches developed a strong sense of corresponding antagonistic patriotism, which did not subside even in the face of the Ottoman threat.

The symbiotic relationship between religious and state institutions endured after the collapse of Byzantium, after the fall of Constantinople in 1453. One of the biggest dilemmas the Ottoman authorities faced was to maintain their rule over an overwhelming majority of Christian subjects. With forceful conversion not being an option, the policy that prevailed was to assimilate Christians into the Ottoman state by granting religious freedom in exchange for disarmament and a head tax. The patriarch not only was allowed to keep his power over doctrinal matters, but also was given considerable civil authority. Orthodox bishops literally functioned in their dioceses as administrative and ecclesiastical authorities over Christian populations. Passive cooperation thus achieved, the Sultan sought to achieve active participation as well. Gradually, he implemented a policy that required Balkan Christians to supply the Sultan with boys from the communities at regular intervals. These youths were to be converted to Islam, provided with excellent educational opportunities, and then drafted into civil or military service. In this manner, the youths became a privileged governing class and a central part of the Ottoman administrative structure. Illustrative of this recruitment process, along with its effects on social and religious manifestations of identity, is the story of George Castriot Skanderberg, the son of a prominent feudal lord in what is now Albania. At the age of 18, he was recruited by the Ottoman authorities along with his two brothers, and received religious and military training in Ottoman institutions. Subsequently, he joined the Ottoman military and participated in numerous campaigns, rising to a senior military rank. Unlike his brothers, however, Skanderberg became a renegade officer, organized a series of successful military campaigns against the Ottomans in his place of birth, and converted back to Christianity. Skanderberg died in 1468 and eventually became modern Albania’s national hero, not because of his altering of religious identity, but for his local patriotism. Without much prospect for victory, however, most of Skanderberg’s followers converted to Islam after their leader’s death.

In the 19th century, the political and economic decline of the Ottoman Empire and modernization pressures from Western Europe produced popular dissatisfaction in Southeast Europe. This in turn increased the Ottoman authorities’ reliance on violence to maintain control. The shift in the style of governance caused emerging political elites to make demands for national self-determination. As national revolutions began taking over Ottoman authorities, thus setting the process of Imperial disintegration, the Ecumenical church found itself under regional pressures to grant regional institutional autonomy.

The first such case was with the Serbian church. Following the creation of an autonomous Serbian state in 1830, it requested and received approval for autonomous status. In 1920, the Serbian national church established its own Patriarchate. Not long after the establishment of the Serbian autonomous church, political and religious authorities in the newly created Greek state, declared the establishment of the autonomous Greek national church. By 1950, the Patriarchate in Istanbul also recognized its autonomous status. The Romanian national church was declared independent from the Patriarchate in Istanbul in 1864. In 1925, it established its own Patriarchate. In 1870, Bulgarian national leaders requested and were given permission by the Sultan to set up autonomous religious institutions, even prior to the creation of the Bulgarian state starting in 1876. By 1951, the Bulgarian national church was elevated to the Bulgarian Patriarchate as well. Accordingly, when Albania was proclaimed an independent state in 1912, it declared an autonomous Albanian national church nine years later despite the fact that the majority of Albanians had converted to Islam. Similarly, the establishment of a Macedonian national identity was followed by the establishment of the autonomous Macedonian national church in 1945. By 1967, this church was also elevated to the status of Patriarchate —not in relation to the Ecumenical Patriarchate in Istanbul, but in relation to the Serbian Patriarchate.

One can gauge the significance of these developments in the context that the title of the Patriarch in the Orthodox denomination of Christianity is the same as the title of the Pope in the Catholic denomination. More importantly, at no single instance have any of these churches deviated from the nationalistic agenda of their state or the people they are serving. Thus, the religious institutions often maintain far more assertive nationalistic outlooks than non-religious institutions.