In addition to establishing the new social structure, the early Romanov tsars faced and easily defeated the only challenge to the tsar's authority that the Orthodox Church ever presented. Under Mikhail, the position of patriarch became exceedingly powerful and influential, largely because Mikhail's father, Filaret, was patriarch during his son's reign. Not surprisingly, the young tsar relied heavily on his father's guidance, although scholars are divided on how completely Filaret dominated his son. It is clear, however, that Mikhail valued his father's opinion and that Filaret wielded a great deal of power in his own right: he took the title Great Sovereign and received foreign embassies in his own court. It is likely that Filaret was a very valuable advisor to Mikhail—Filaret had been one of the contenders for the throne during the Time of Troubles and was politically very astute. This cooperation between ruler and patriarch set an example that future patriarchs sought to emulate. At the same time, the Church was undergoing an internal reformation that led to heated debates over the proper way for Russian Orthodox to worship. The reformers wanted to purge the Church of all inaccuracies and impurities that it had acquired over the years and to improve public morality by closing shops and taverns on Sundays and banning strolling musicians who sang bawdy songs. In addition to the new restrictions, however, the Church revised some of its rituals and practices in order to come into line with the other Orthodox religions: Russians would now make the sign of the cross with three fingers instead of two fingers, priests would wear Greek-style vestments, and some details of the liturgy were revised with new prayer books published to reflect these changes. These few changes led to a deep schism in the Church between those who called themselves "Old Believers," who insisted on using the old symbols and liturgy, and the rest of the Orthodox, who adopted the changes.
These conflicts came to a head under the leadership of Patriarch Nikon, appointed by Alexei in 1652. Nikon continued reform of the Church, and under his guidance, with the full support of the tsar, the changes became mandatory. This angered many Russians, who rebelled and refused to adopt the new practices. At the same time, Nikon himself made many enemies in the Church and among the elite because of his arrogance and vengeful attitude toward any who opposed him. He also angered Alexei by assuming more power than Alexei was willing to bestow upon him, even taking the title "Grand Sovereign" in imitation of Patriarch Filaret Romanov. Eventually, the tsar and patriarch had a disagreement, which sent Nikon in a huff from the city. Alexei had him tried in an ecclesiastical court for abandoning his post and exiled Nikon to a distant monastery. The tsar was acknowledged as the undisputed leader of both Russia and the Orthodox Church. Never again would a Church leader openly defy the tsar.