Saratov was founded in 1590 as a watch fortress by Moscow shooters. Until the establishment of the Saratov-Penza Diocese in 1799, the city was under the jurisdiction of the Astrakhan bishops in church matters. The first wooden Trinity church on the site of the current cathedral was built with the blessing of the Astrakhan bishop Parfeniy in 1674-1675. It was erected quickly in the only square of Saratov, but ten years later, in 1684, it burned down in a fire. Protopope Ignaty Danilov and the brotherhood appealed to Metropolitan Savvatiy of Astrakhan and Terek for permission to build a new church on the same site.

The correspondence with the Astrakhan episcopal house lasted five years, and only in June 1689 did Metropolitan Savvatiy send permission for construction to Saratov, specifying some design features of the future church. Construction began quickly thanks to the efforts of the city's residents, and by 1694 the church was ready for consecration. In October 1695, it was inspected by Archimandrite Iosif from Astrakhan. The inspection act mentioned the name of the first rector, Protopope Grigory Spiridonov, and described the wooden roof and bell tower with bells of different weights.

In October 1695, Archimandrite Iosif consecrated both churches of the cathedral: the upper in honor of the Holy Trinity and the lower in honor of the Dormition of the Mother of God. The acceptance act noted the oven in the refectory of the lower church, which was a novelty for provincial churches of that time. Perhaps, in winter, services were held in the warm refectory, while in summer in the unheated part of the church. The clergy of the cathedral faced difficulties due to the small number of parishioners. Rector Ignaty Danilov appealed to Peter the Great for a land grant, and in 1696 the sovereign ordered a plot of land to be allocated to the church.

On October 26, 2016, a wedding ceremony took place at the Holy Trinity Cathedral in Saratov, and for the first time in 99 years in Russia, civil marriage registration was conducted by the registry office staff.