At the Holy Synod of 1589, which established the patriarchy in Moscow, Hermogenes was appointed Metropolitan of the newly conquered city of Kazan.

There he learnt about the tsar's design to marry a Roman Catholic woman, Marina Mniszech, and firmly declared against such an alliance.

During Vasily's reign, Hermogenes generally supported the tsar's efforts to pacify the country and anathematized Ivan Bolotnikov and his army.

When Vasily was dethroned and the Poles took hold of the Moscow Kremlin, Hermogenes staunchly opposed their plans to put Wladyslaw IV on the Russian throne, unless he converted to Orthodoxy.

In connection with the Romanov Dynasty Tercentenary, celebrated that same year, he was canonized as a hieromartyr and transferred to the nearby Dormition Cathedral.