In 1989, a church community consisting of 111 residents was registered in the village of Varnitsy. The parish churches of the Resurrection of Christ and Saints Paisius and Uar, located near the Varnitsky Monastery, were transferred to the church and renovated by the inhabitants of the Trinity-Sergius Lavra.

In 1992, in honor of the 600th anniversary of the repose of St. Sergius of Radonezh, a wooden chapel was erected on the site of the destroyed Trinity Cathedral, and a canopy was built over the ancient holy well.

In 1995, by the decree of His Holiness Patriarch Alexy II and at the request of Archbishop Mikhail of Yaroslavl and Rostov, the Varnitsky monastery came under the protection of the Trinity-Sergius Lavra, and restoration work began. The churches were returned part of the monastery premises.

In 2000, the construction of a new Trinity Cathedral began, which was to resemble the demolished one.

In 2001, the restoration of the Introduction Church was completed, and the fence with the gate church and service and residential buildings were restored.

By July 2003, the monastery had erected the Trinity Cathedral with a four-tier bell tower, a two-story refectory building, and three walls with towers.

In 2002, an Orthodox gymnasium named after St. Sergius opened in the Varnitsky settlement. In 2005, a branch of the gymnasium with dormitory accommodation for students in grades X-XI was established within the monastery itself.

On July 29, 2003, the gate church was laid.

In 2014, His Holiness Patriarch Kirill of Moscow and All Russia consecrated the Cathedral of St. Sergius of Radonezh, which became the main church of the monastery.