The history of the monastery begins in 1385 with the founding of the Trinity Desert, created in honor of the reconciliation of the princes of Moscow and Ryazan. This is one of the revered places of St. Sergius of Radonezh. According to legend, a wounded warrior from the Battle of Kulikovo was healed by drinking water from a local spring and chose to live here. In a vision, he was visited by Sergius of Radonezh, who blessed the creation of the monastery, saying: "Let God's will be fulfilled here."

The first documented mention of the Holy Spirit Monastery dates back to the late 1620s when it was called the Monastery of the Holy Life-Giving Trinity. It was not wealthy and was abolished in 1764 by the decree of Catherine II, and a charitable institution was opened in its place. In 1786, monks from the burned-down Ryazan Spirit Monastery were transferred here, and the monastery was restored under the name Holy Spirit Monastery.

The monastery had two churches. The first, in honor of the Vladimir Icon of the Mother of God, is considered older and, according to tradition, was the household church of the Romanov boyars. The second church, of the Descent of the Holy Spirit, was founded no later than the early 17th century. The last building was constructed in 1880; it is a five-domed church in the neo-Russian style with a refectory and chapels dedicated to Nicholas and Elijah. The bell tower was erected in the early 19th century. The monastery had the abbot's quarters with a brotherly refectory and garden, a two-story stone brotherly building built between 1818 and 1830, a stone bathhouse, a granary, a wooden icehouse, and a stone cattle yard. All these structures were erected under the abbots Arkady and Pavel between 1830 and 1832. In the 19th century, the monastery was sparsely populated.

The monastery was closed in 1918 after the revolution. The buildings were partially destroyed and partially repurposed. In 1921, the first Soviet trade union school in the city was opened here, followed by an agro-technical point, and from 1937, a party school. During the war, the buildings were used as an orphanage and later as a boarding school.

Although there are no historical records of burials in the monastery cemetery, two graves have been preserved: that of Nadezhda Alexeyevna Khudekova, the wife of the famous playwright and ballet historian Sergey Nikolaevich Khudekov, and the illustrator Pyotr Mikhailovich Baklevsky.

Today, the Holy Spirit Archpriest's Courtyard of the city of Skopino in the Ryazan region is located in the monastery, belonging to the Skopino Diocese of the Russian Orthodox Church of the Moscow Patriarchate.

On July 20, 2013, the household church in honor of the Holy Martyr Ignatius, Bishop of Skopino, was consecrated, where services are held.