The abbey stood in ruins until 1471, when two sons of Marfa Boretskaya were killed by a vicious storm and their bodies were recovered on the beach near the monastery twelve days later.
On 24 August 1553, a ship of Richard Chancellor reached the salt-mining settlement of Nenoksa, which is still famous for its traditional wooden architecture.
The Nikolo-Karelsky Monastery flourished after the establishment of the Muscovy Company, as the bulk of their trade passed through the local harbour.
In August 1618, the harbour was visited by John Tradescant the elder, who conducted a survey of an island situated opposite the monastery.
The five-domed cathedral of St. Nicholas was built in 1670–74, preceded by the Assumption church (1664–67), to which it is joined by a gallery.