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Schism with the Old Believers

In 1653, Patriarch Nikon established a series of reforms that aimed to bring the practices of the Russian Orthodox Church into line with its Greek counterpart. Most notably, the church began to mandate the use of three fingers instead of two in making the sign of the cross. This resulted in significant dissent among the church community. Nevertheless, Alexis continued to support Nikon until 1658, when Nikon abandoned his post due to a personal insult, leaving the seat of the patriarch vacant.

In 1666, the tsar convened the Great Moscow Synod, which was attended by Patriarch Macarius III Ibn al-Za'im and Patriarch Paisius of Alexandria, in order to address the problems caused by Nikon. The synod agreed to formally depose Nikon, and also decided to excommunicate all who opposed the reforms of the church; those opponents broke away from the official Russian Orthodox Church to form the Old Believers movement.

Across Russia, Old Believers were harshly persecuted. One such old believer was Avvakum "the leader of the old Believers". Avvakum "had his wife and children buried alive in front of him; he himself was just exiled".

Several old believers fled to the monastery of Solovki which had revolted in the Solovetsky Monastery uprising. The monastery would be besieged for seven years until 22 January 1676 which was a few days before Alexis's death on 8 February 1676.