The church dedicated to Saint Alexius, Metropolitan of Moscow, was built in 1914 and became part of the Church of the Ascension of the Lord in the village of Zimovye, Cherepanovo District. In the 1930s, clergy faced repression, and the church was used as a club, a pioneer house, and later as a House of Children's Creativity, where the stage was located in the place of the altar, until the building was transferred to the ownership of the Novosibirsk Diocese.

In the 1990s, residents of Cherepanovo repeatedly appealed to the district administration to return the church building, but to no avail. Only on March 30, 2006, did the deputies of the Cherepanovo District decide to transfer the building to the diocese. The restoration of the church was undertaken by Archimandrite Kirill Skakal'skiy and the brotherhood of the monastery in honor of All Saints who shone in the land of Siberia, with the support of the district administration. The first Divine Liturgy took place on Christmas in 2008, and since then, services have become regular.

In the autumn of 2008, the administration transferred to the diocese the adjoining part of the House of Children's Creativity, covering an area of 440 square meters, which needed repairs. Subsequently, it housed a refectory, library, accounting office, Sunday school, youth club, carpentry workshop, and garage.

In May 2010, a mosaic icon of the Savior was installed on the facade of the church. In April 2011, with the blessing of Archbishop Tikhon, the construction of the bell tower began, which was completed in the summer by the efforts of the monastic brotherhood. On April 5, 2012, Bishop Luka of Iskitim and Cherepanovo consecrated the bells, and on April 8, the first archpastoral liturgy was held under his guidance.

On May 21, 2012, the Church of Saint Alexius in Cherepanovo was granted the status of a cathedral church by the resolution of His Holiness Patriarch Kirill of Moscow and All Russia.

Since June 2014, with the blessing of Bishop Luka, students of the icon painting department of the Novosibirsk Theological St. Macarius Institute began painting the church. On October 17, 2014, a solemn celebration of the 100th anniversary of the Church of Saint Alexius took place.