Upon the death of Patriarch Joseph in 1652, Vonifatiev was lawfully elected Patriarch, but refused the position. The Tsar Alexei then put Nikon in his place, contrary to the Church Canons, which forbade the Tsar to have such influence over the appointment. Apparently no one actively contested the appointment and Nikon commenced his reign with several reformatory measures. No sooner did Nikon become Patriarch in Moscow than he began to enforce the reforms vigorously, quite different from what the "Guardians of Piety" had expected. He took Greek texts, recently printed in Italy (in Roman Catholic publishing houses), as the pattern for his reforms. The Greek Orthodox Church, by now under Muslim rule and deprived of its privileges and power, had began to seek union with the Pope of Rome-the very symbol of [[heretic|heresy]] for Eastern Christians during previous centuries. Then, with the long arm of Russian law he tried to force everyone to accept them. In 1653, he sent a memorandum to the churches in the land which instructed them in various revisions of the services and the books. These reforms met with opposition from many of the clergy. Among the major points which were contested were: (1) how many fingers would be used to make the sign of the cross; (2) the spelling of Jesus' name; (3) whether "Alleluia" should be sung two or three times; (4) the retention of certain words and phrases in the Creed; (5) the number of hosts to be used in the liturgy; and (6) whether the priests should walk around the altar with or against the passage of the sun. These matters of ritual, seemingly unimportant in themselves, nevertheless were the embodiment of certain theological precepts and ideological alliances, and hence stirred considerable controversy upon their arrival. For example, the conservatives maintained that the sign of the cross with two fingers rather than three (the latter being the proposed reform) signified the dual nature of Christ, with the first finger representing the divine nature and the bent second being a symbol of Christ's descent to Earth for the salvation of humankind. They cited many old icons to support their position on this matter, in which some of the saints and Christ could be seen using the two-fingered sign. The three-fingered sign, on the other hand, was intended as an acknowledgment of the Trinity. But this was considered by the conservative dissenters to represent Greek heresy. To make matters worse, many of the clergy felt that strict observance of the most minute details of the dogmas and disciplines of the church were necessary to salvation. This was a direct result of the reformatory efforts of the group in Moscow.

However, his compatriots continued to wield official power, and the persecutions went on in his absence. The Tsar was on the side of the would-be reformers and began to openly wage campaigns against the conservatives. After the Council of 1666, in which the Stoglav of 1551 was declared a forgery and heretical, the Solovetski Monks of the White Sea formed a bastion against the new tide of reform, and were promptly excommunicated and eventually replaced with monks from Moscow.