In 1618, the Grand Hetman of Lithuania Jan Karol Chodkiewicz (Jonas Karolis Chodkevičius) started the construction of a small church for the Benedictine nuns in Vilnius.

After the fire, the reconstruction of the church was led by the architect Johann Christoph Glaubitz, who was contracted by the mother superior of the monastery, Joana Sibilė Reitenovaitė.

He designed the church's current appearance: the towers were raised (up to 5 storeys), ornate pediments were built, vaulted ceiling was redone, and the chapel was rebuilt.

The church was severely damaged in 1812 during the French invasion of Russia and later during World War II and many valuable works of art were lost.

In 1945, the remaining nuns were deported by the Soviet authorities and a warehouse was set up in the church, which later was transferred to the Vilnius Art Museum.