The monastery was founded in 1689 in the second half of the 17th century on the left bank of the Sura River, not far from the fortress. It is the oldest monastery in the city. In 1880, the Penza architect Mikhail Andreyevich Rudkevich reconstructed it, building a two-story stone church of the Transfiguration of the Lord, known as the Spaso-Transfiguration Church.

After Catherine's secularization reform, the monastery was left without state support. In 1765, monks from the abolished Moksha Kazan Monastery were transferred here, led by Hieromonk Pitirim, and in 1798, brothers from the abolished Ferapontov Monastery in the Novgorod Diocese. In 1794, at the request of the townspeople, the monastery was moved beyond the then city limits to a site where a cemetery and the stone Church of the Ascension were located.

In the spring of 1922, the Soviet authorities confiscated church property in the Spaso-Transfiguration Monastery twice, in March and April. In 1925, the monastery's necropolis ceased its activities and was soon liquidated, with the cast-iron tombstones melted down. The last burials in the cemetery were destroyed in the early 1960s.

On September 21, 2013, the remains of the famous Russian philanthropist Maria Kiseleva and her husband, discovered at the site of the destroyed Trinity Church, were reburied in a chapel built on the site of the monastery cemetery in 2003.