In 1693, the Yaroslavl merchant Ivan Kemski ordered the construction of two churches on opposite banks of the Volga at his own expense. One was dedicated to the holy Zosima and Savvatiy, and the other, the Ascension-Blessed Virgin Church. These churches served as beacons for crossing the Volga. The route through the Zosima and Savvatiy Church led from Yaroslavl north to Kostroma and Vologda. Every traveler considered it their duty to visit this church. It is known that Emperor Nicholas I visited it during a trip to Kostroma, as did the writer M.Yu. Lermontov. In 1771, with the funds of parishioners, another stone summer church was built next to the Zosima and Savvatiy Church in honor of the Life-Giving Trinity, with two chapels: of the Prophet Elijah and St. Nicholas the Wonderworker.

In the 1930s, during the persecution of the Russian Orthodox Church, the large church complex was closed, and the Trinity Church was destroyed to the ground. The Zosima and Savvatiy Church miraculously survived, although it was vandalized. Various workshops were housed here, then a laundry, and by the 1980s, the church fell into disrepair and turned into ruins.

In 1998, the ruins of the Church of Saints Zosima and Savvatiy, the only church in the diocese dedicated to the saints of the Far North, were transferred to the Yaroslavl Diocese. In 2002, a chapel in honor of the holy Zosima and Savvatiy was established and consecrated next to the church, where the first Christmas service took place on January 7, 2011.

At the end of 2008, restoration work began on the church, which was literally being raised from the ruins. The buildings barely resembled a church, and the bell tower was destroyed. Major work was done to strengthen the foundation and vaults, the roof was renewed, the bell tower was restored, and domes were installed. The bell tower stands out with its unusual architectural solution: a wide octagon, arcades, and another smaller octagon topped with a tent. However, repair and restoration work continues, with interior finishing and the installation of necessary communications ongoing.

On April 24, 2011, on Easter, the first service was held in the church, and since then, services have become regular.

By the blessing of Metropolitan Panteleimon of Yaroslavl and Rostov, in 2012, the Church of Zosima and Savvatiy was granted the status of a regional Naval Church. The Yaroslavl branch of the All-Russian Movement for the Support of the Navy decided to build a memorial near the church in memory of the fallen sailors from Yaroslavl and to immortalize the holy righteous Theodore Ushakov with a large icon at this memorial.