Tsar Feodor I made a grant of Shenkursk to his brother-in-law, Boris Godunov, who bequeathed it to his future son-in-law, Johan of Schleswig-Holstein, who died shortly after arriving to Russia. The Romanovs presented the area to Prince Dmitry Troubetskoy as his "votchina". Upon his death, the town was returned to the crown. In 1640–1643, the Tsar ordered a new fortress to be built in Shenkursk. Catherine the Great chartered Shenkursk in 1780, and Shenkursk became the seat of the newly established Shenkursky Uyezd in Vologda Viceroyalty (from 1796, in Arkhangelsk Governorate).