By the 1860s the fort had lost its military value and was being used for ammunition storage. It was struck from the military register in 1896. On 26 January 1897 the St. Petersburg Institute of Experimental Medicine took over the fort and established a laboratory there to research the plague, with veterinary doctor M. G. Tartakovsky its first director. Work was hazardous and there were outbreaks of plague among the human staff in 1904 and 1907, with the facility finally being closed in 1917 and the fort being returned to the Navy.
The fort was stripped of its fixtures and abandoned in 1983. Some restoration work was begun in 2005 when the fort was leased by a commercial firm.