Peter also reforms the government of the Orthodox Church, whose traditional leader is the Patriarch of Moscow.

When the office had fallen vacant in 1700, Peter had refused to name a replacement, allowing the Patriarch's Coadjutor (or deputy) to discharge the duties of the office.

Twenty-one years later, Peter follows the advice of Ukrainian clergyman Feofan Prokopovich, bishop of Pskov, and in 1671 erects a spiritual college, namely the Holy Synod, a council of ten clergymen, to take the place of the Patriarch and Coadjutor, which he permanently abolishes.

The tsar appoints a secular official—the ober-prokuror, or chief procurator— to supervise the activities of the Holy Synod's activities, which ferociously persecuted all dissenters and conducted a censorship of all publications.

Priests officiating in churches are obliged by Peter to deliver sermons and exhortations that are intended to make the peasantry “listen to reason” and to teach such prayers to children that everyone would grow up “in fear of God” and in awe of the tsar.

The regular clergy are forbidden to allow men under thirty years old or serfs to take vows as monks.

The church is thus transformed into a pillar of the absolutist regime.

Partly in the interests of the nobility, the extent of land owned by the church is restricted; Peter disposes of ecclesiastical and monastic property and revenues at his own discretion, for state purposes.