The Holy Spirit Monastery is first mentioned in chronicles from 1162. By the end of the 16th century, three stone churches stood on its territory: the Church of the Holy Spirit, the Church of the Trinity, and the Church of St. Nicholas the Wonderworker. However, in the late 18th century, like many other monasteries, it was abolished, and the monks were transferred to Valaam.

In 1786, the monastery was restored, but as a women's monastery. It existed in this form until the revolution, belonging to the 1st class of monasteries in Russia. Today, of all the buildings, the Cathedral of the Descent of the Holy Spirit, the Church of the Life-Giving Trinity with the refectory, and several other buildings remain, one of which houses the State Historical Archive of the Novgorod Region.

The monastery did not suffer significant destruction, although some paintings in the interiors have been lost. The Church of the Trinity was restored in 1963, and the Cathedral of the Holy Spirit was restored in 1984-1985.

The Holy Spirit Monastery has been repeatedly devastated but has always been restored, and many relics were preserved within its walls until recently. In 1913, the relics of Euphemia the All-Praised and St. Moses, as well as his staff, were located here. The monastery also housed miraculous icons of St. Nicholas, painted around 1500, and the Descent of the Holy Spirit upon the Apostles, dated no later than 1357. The current location of these relics is unknown.

The Cathedral of the Holy Spirit is a four-pillar, single-domed, two-story church from the late 19th century, designed in the "Neo-Russian" style, which is rarely found in the Novgorod region. The Church of the Trinity is a small, pillarless church with a refectory on the western side, whose facades resemble Novgorod buildings from the mid-16th century. The refectory contains utility and cult premises, the architecture of which combines local and Moscow traditions.

In the early 1920s, the monastery was closed, and the cathedral was transferred to the Gubarkhiv Bureau in 1926 to create a storage facility. During the Great Patriotic War, the German authorities used the cathedral as a warehouse. Today, the street on which the monastery complex is located is named Dukhivskaya after Musa Jalil.