Under Dmitry Donskoy, the Kamenny Monastery was run by Dionisius, a Greek monk who introduced the coenobian rule of Mount Athos, whereby the brethren were closed alike, took their meals (usually limited to bread and scarce vegetables) in the refectory and were bound to possess no private property.

Ivan III's brother Andrey Menshoy, who was the ruler of Vologda, commissioned a stone four-pillared cathedral to be built on the island.

In the 16th century, the Kamenny Monastery did not develop as quickly as the two last-mentioned abbeys, because of the limited territory that the tiny and remote island could afford.

The regional administration profited from the situation to blow up the oldest building of the Russian North in order to obtain brick required for construction of the local "palace of culture", which eventually failed to materialise.

[1] As of 2015[update], the only building marking the spot of the historic monastery is the church belltower from the 1540s, which is now being repaired by a team of enthusiasts from Vologda and Moscow.

In October, 2017, the Holy Synod of the Russian Orthodox Church officially decided to reopen Spaso-Kamenny Preobrazhensky monastery with Dionysius (Vozdvizhenskiy) as hegumen.