The church in the village of Maloe Perekopnoye was built in 1833 with funds from the parishioners. The building was made of stone, as was the bell tower, with one altar in the name of the Holy Life-Giving Trinity. The church was unheated and could accommodate 345-390 people. At the time of its construction, the village was part of the Nikolaevsky district of the Saratov province. In 1843, a rural public school was opened at the church, located in the church watchman's house, and in 1863 it became a zemstvo school. In May 1868, a Sunday school began operating at the temple.

In 1887, a project for the expansion of the church was developed and approved on June 19 by the Construction Department of the Samara Provincial Administration. However, due to insufficient expansion, the project was not approved by the Diocesan Administration. Later, a new project was proposed, which required the demolition of the refectory and bell tower, the expansion of the church, and the construction of a new bell tower. This project was approved on August 5, 1891, and received the approval of the Diocesan authorities. The church was planned to have three altars.

Construction was carried out solely on donations from parishioners and was completed in 1897. The three-altar church became heated and could accommodate up to 1,500 people. Ten fathoms from the church stood a wooden watchman's house. Both buildings were insured against fire for 29,000 rubles. The main altar was consecrated on September 27, 1897, and the altars in the right and left chapels on November 1 and 2, 1901, respectively. In 1898, a church-parish school opened in the watchman's house.

During the Soviet era, after administrative changes on July 15, 1928, the village of Maloe Perekopnoye became part of the Saratov region. Services in the church continued until 1935, after which it was closed.

Reconstruction began in 1997. On November 1, 2001, the centenary of the church was celebrated. On December 13, 2003, Archpriest Vitaly Shovgor performed the Rite of Placement of the Holy Antimension in the restored right chapel. The complex now includes the church building and the rectory. The church is a monument of regional architectural significance. The restoration was initiated by local residents, with significant assistance from V.V. Volodin. On October 2, 2010, Bishop Longin of Saratov and Volsk performed the Great Consecration of the church.