Most of the empire's subjects were not Orthodox. Catherine II abandoned forced conversion in the 1770s and in 1788 established at Orenburg a Muslim Spiritual Assembly with a state-appointed mufti, examining and licensing prayer leaders and adjudicating family disputes. Robert Crews argues that this made the tsarist state a participant in Islamic religious life, and that Muslim subjects used it: litigants brought their internal disputes to imperial officials and asked the state to enforce the sharia as they understood it, so that the empire became an arbiter of Muslim orthodoxy rather than merely its supervisor.
Other communities were handled more harshly. The Greek Catholic churches of the western provinces, in communion with Rome, were absorbed into Orthodoxy by decree in 1839 and again in 1875, with resistance broken by force. Jews, some five million by the end of the century, were confined to the Pale of Settlement, restricted in schooling and occupation, and left unprotected in the pogroms of 1881 and 1882 and again in 1903 to 1906, which drove mass emigration and gave Zionism much of its early impetus.
The edict of toleration of April 1905 finally allowed subjects to leave Orthodoxy legally. In August 1917 a council of the Russian church met for the first time since the seventeenth century and restored the patriarchate, electing Tikhon in November, weeks after the Bolshevik seizure of power that would place the whole institution under a state committed to atheism.