Nikon (Nikita) was born in the village of Veldemanovo, near Nizhny Novgorod, the son of a peasant of Finnic stock. After acquiring the rudiments of an education in a nearby monastery, Nikon married, entered the clergy, was appointed to a parish in Lyskovo, and then settled in Moscow. The death of all three of his children moved him to seek repentance and solitude. For the next 12 years, from 1634 to 1646, he lived as a monk (it was at this point that he adopted the name Nikon), as a hermit, and finally as an abbot in several northern localities. In 1646 he went on monastic business to Moscow, where he made so favourable an impression on the young tsar Alexis and on Patriarch Joseph that they appointed him abbot of the Novospassky monastery in Moscow, the burial place of the Romanov (Romanov Dynasty) family.

During his stay there, Nikon became closely associated with the circle led by the tsar's confessor, Stefan Vonifatyev, and the priests Ivan Neronov and Avvakum Petrovich (all, like him, natives of the Nizhny Novgorod region). This group of priests strove to revitalize the church by bringing about closer contact with the mass of the faithful, and they also sought to purify religious books and rituals from accidental errors and Roman Catholic (Roman Catholicism) influences. With their backing, Nikon became first metropolitan of Novgorod (1648) and then patriarch of Moscow and all Russia (1652).

Nikon accepted the highest post in the Russian church only on condition that he be given full authority in matters of dogma and ritual. In 1654, when the tsar departed for the campaign against Poland, he asked Nikon to supervise the country's administration as well as watch over the safety of the tsar's family, and in 1657, with the outbreak of the new war with Poland, he invested Nikon with full sovereign powers. Enjoying the friendship of the tsar, the backing of the reformers, and the sympathy of the population of Moscow, Nikon stood at the pinnacle of his career.

It was not long, however, before Nikon alienated his friends and infuriated his opponents by his brutal treatment of all those who disagreed with him. On assuming the patriarchate, he consulted Greek scholars employed in Moscow as well as the books in the patriarchal library and concluded not only that many Russian books and practices were badly corrupted but also that the revisions of the circle of Vonifatyev had introduced new corruptions. He then undertook a thorough revision of Russian books and rituals in accord with their Greek models, which he believed were more authentic, to bring them into line with the rest of the Orthodox church. Assisted by Greek and Kievan monks and supported by the Greek hierarchy, he next carried out several reforms of his own: he altered the form of bowing in the church, replaced a two-fingered manner of crossing oneself with a three-fingered one, and ordered that three alleluias be sung where Moscow tradition called for two. A council of the Russian clergy that he convened in 1654 authorized him to proceed with the revision of liturgical books. He next began to remove from churches and homes icons that he considered incorrectly rendered. To quell mounting opposition to these moves, he called in 1656 another council, which excommunicated those who failed to adopt the reforms.

Though all the changes introduced by Nikon affected only the outward forms of religion, some of which were not even very old, the population and much of the clergy resisted him from the beginning. The uneducated Muscovite clergy refused to relearn prayers and rituals, while the mass of the faithful was deeply troubled by Nikon's contempt for practices regarded as holy and essential to Russia's salvation. His former friends spoke out against him, especially Avvakum Petrovich, who would lead the struggle against Nikon and proclaimed that the patriarch's decisions were inspired by the devil and filled with the spirit of Antichrist. This was the origin of the Raskol, or great schism within the Russian Orthodox Church. Yet what really brought about Nikon's downfall was the hostility of the tsar's family and the powerful boyar (aristocratic) families, who resented the high-handed manner in which he exercised authority in the tsar's absence. They also objected to his claims that the church could intervene in affairs of state but was itself immune to state interference. Nikon believed that the church was superior to the state because the heavenly kingdom was above the earthly kingdom. He also published a translation of the Donation of Constantine (a medieval forgery that claimed that the emperor Constantine had bestowed temporal and spiritual power on the pope) and used the document to support his claims to authority.

When Alexis returned to Moscow in 1658, relations between tsar and patriarch were no longer what they had been. Grown in self-confidence and incited by relatives and courtiers, Alexis ceased to consult the patriarch, though he avoided an open break with him. Nikon finally struck back after several boyars had insulted him with impunity and the tsar failed to appear at two consecutive services at which Nikon officiated. On July 20 (July 10, O.S.), 1658, in characteristically impetuous fashion, he announced his resignation to the congregation in the Assumption (Uspensky) Cathedral in the Kremlin, and shortly afterward he retired to the Voskresensky monastery.

Nikon had apparently hoped by this act to compel the tsar, whose piety was well-known, to recall him and to restore his previous influence. This did not happen. After several months in self-imposed exile, Nikon attempted a reconciliation, but the tsar either refused to answer his letters or urged him to formalize his resignation. Nikon refused to do so on the ground that he had resigned merely from the Moscow see, not from the patriarchate as such. For eight years, during which Russia was effectively without a patriarch, Nikon stubbornly held on to his post, while Alexis, troubled by lack of clear precedent and by the fear of damnation, could not decide on a formal deposition. Finally, in November 1666, Alexis convened a council attended by the patriarchs of Antioch and Alexandria to settle the dispute.

The charges against Nikon were presented by the tsar himself. They concerned largely his behaviour in the period of the tsar's absence from Moscow, including his alleged arrogation of the title of “grand sovereign.” Many of the charges were entirely without foundation. The Greek hierarchy now turned against Nikon and decided in favour of the monarchy, whose favours it needed. A Greek adventurer, Paisios Ligaridis (now known to have been in collusion with Rome), was particularly active in bringing about Nikon's downfall. The council deprived Nikon of all his sacerdotal functions and on December 23 exiled him as a monk to Beloozero, about 350 miles (560 km) directly north of Moscow. It retained, however, the reforms he had introduced and anathematized those who opposed them and who were henceforth known as Old Believers (Old Believer) (or Old Ritualists). In his last years, Nikon's relations with Alexis improved. The successor of Alexis, Fyodor III, recalled Nikon from exile, but he died while en route to Moscow.

Nikon was one of the outstanding leaders of the Russian Orthodox Church and an able administrator. His ultimate failure was due to two main factors: (1) his insistence on the hegemony of church over state had no precedent in Byzantine or Russian traditions and could not be enforced in any event; and (2) his uncontrollable temper and autocratic disposition alienated all who came in contact with him and enabled his opponents first to disgrace and then to defeat him.