The history of the monastery in Kuzhener begins with the discovery of a holy spring with cold and clear water in the Kuzhener grove at the end of the 19th century. Local residents used the water from the spring for healing various ailments. As a sign of this, a post with an icon of Saint Panteleimon was erected at the spring. The village priest, Father Nikolai from Toktay-Belyak, made the first pilgrimage here and held a prayer service, predicting the construction of a church or monastery. In September 1884, a stone chapel was built over the spring, where services were held three times a year. Residents requested the establishment of a women's community in the name of Saint Nicholas the Wonderworker. The organization of the monastery was taken up by the novices from the Sviyazhsky John the Baptist Monastery. The first to settle near the chapel was Ekaterina Smolentseva, and in the spring of 1897, Bishop Alexy of Vyatka blessed the sisters. The authorities granted the request to transform the chapel into a church.

In September 1897, the laying of the altar and porch at the chapel began. Nun Lyudmila from the Vyatka Transfiguration Monastery organized a choir. A year later, the Church of Saint Nicholas the Wonderworker was consecrated, and the community began its activities. Local peasants actively supported the community. In the summer of 1900, merchant Fyodor Yakovlevich Roshchin began to assist the residents. In June 1901, Mother Lyudmila arrived with the sisters, and the monastery began its life. On December 31, 1901, the Holy Synod officially established the Kuzhenersk-Nikolayev community. The nuns and novices introduced Mari girls to Orthodox culture. Cells and workshops were located in a wooden building. The fame of the Kuzhener monastery spread, and the number of pilgrims grew. The church could not accommodate everyone, so F.Y. Roshchin invited architect Charushin to design a new church. On August 16, 1904, the laying of the Transfiguration Cathedral began, which was completed in 1909. The church has not survived, but photographs show it in the old Russian style.

In May 1910, the Synod transformed the community into a women's monastery, with Nun Lyudmila as the abbess. The monastery housed 127 residents. A stone refectory was built, the building of which has survived. In 1907, the construction of a wooden fence was completed. By the blessing of Bishop Philaret, an orphanage for girls was opened at the monastery under the guidance of Nun Evnikiya.

By 1914, the monastery had about 200 residents. The monastery had a good economy: land plots, workshops, and a cattle yard. Among the residents stood out Alexandra Obukhova, a talented icon painter. She was awarded for her works, but her fate was difficult. In the 1930s, she was accused of counter-revolutionary activities and exiled for 2.5 years. Alexandra passed away in 1973 and was buried in the village of Yuledur.

During World War I, prayer services for the victory of the Russian army were held at the monastery, but life became harder. In 1916, benefactor F.Y. Roshchin passed away and was buried near the walls of the Transfiguration Church. In 1918, the monastery was closed, Abbess Lyudmila left, and the cathedral was turned into a club. In 1956, the church building was dismantled, and a local cultural center was built from the bricks. For some time after the monastery was closed, services were held in the Nikolsky Church by the spring.

On May 22, 1998, a Divine Liturgy was held in the building of the former refectory of the monastery, and the holy place regained its spiritual life.