After Isidore was condemned for supporting the Union of Florence, Jonah was appointed as metropolitan by a council of Russian bishops at the behest of Vasily II of Moscow.

He was also the first metropolitan in Moscow to be appointed without the approval of the Ecumenical Patriarch of Constantinople, as had been the norm,[3] which marked the beginning of autocephaly of the Russian Orthodox Church.

Despite sporadic Russian attempts to pressure the patriarch of Constantinople into choosing a metropolitan from Russia's native population, most appointees remained Greeks.

[4] Jonah's first effort as metropolitan was to recover the areas lost to the Uniate church, and he was able to add Lithuania and Kiev to his title, but he was unable to gain Galicia.

The influence of Catholicism increased in those regions until Casimir's inclination toward Orthodoxy was repressed and he accepted the demands of Pope Callixtus III.

Jonah also tasked Vassian of the Trinity Lavra of St. Sergius and Kassian of the Kirillo-Belozersky Monastery with the goal of persuading local Russian feudal princes and nobles who resided in Lithuania to continue to side with Orthodoxy, but this attempt failed.