By the end of September, 1689, Peter's rivals were defeated and at the age of seventeen he began to rule Russia. Until his mother's death in early 1694 he would not rule alone, for Natalia, her younger brother Lev Kirillovich, and others of the Naryshkin clan and the larger Naryshkin faction would exercise power together. Peter was not idle, however, for in these years he not only grew up and spent more and more time in the German Suburb, he also began to form the group of favorites, Russian and foreign, on whom he would rely in later years. By the end of the decade, Peter had also captured the Turkish fort at Azov, traveled in Western Europe, and helped lay the foundation for the Northern War against Sweden.

For the time being, it was a Naryshkin government. They began by rewarding their most important allies, the foreign officers, who received a month's pay as a bonus, and the musketeers, who all got a ruble a year as extra salary. Another beneficiary of the new regime was Patriarch Ioakim. He had convinced Peter to arrest Sil′vestr Medvedev as an associate of Shaklovityi in September. At the same time, Ioakim secured an even greater triumph, the expulsion of the Jesuits from Russia.