The date of the church's founding remains unknown. It is difficult to determine the first mention due to the proximity of other churches: St. Nicholas the Wonderworker on Verkhny Dol and the chapel of St. Nicholas the Wonderworker in the Gorniy Monastery. In medieval Vologda, several churches were located in close proximity to each other on Lenivaya Square.

N. V. Falin, referring to the hundredth charter of 1627, suggests that at the site of the current St. Nicholas "Golden Crosses" there could have been "the church of Nicholas the Wonderworker and another church of John Chrysostom."

The name "Golden Crosses" became associated with the church in the 18th century. In 1701, it was still mentioned as "St. Nicholas on the hill." Initially, this referred to the Assumption Cathedral of the Gorniy Monastery. In 1782, in a report from the City Magistrate, the Nicholas Church was referred to as "at the Golden Crosses." After the fire of 1761, when the vaults and domes of the Assumption Cathedral were damaged and lost their gilding, the name transferred to the Nicholas Church, which became known as Nicholas on the Hill, "Golden Crosses." In the book by I. K. Stepanovsky from 1890, the church is mentioned as "Nicholas at the Golden Crosses." The temple was closed in 1930 and later used as a dormitory, auto repair shop, and DOSAAF garages. By 2011, the church was abandoned, the interiors were destroyed, windows broken, the dome and the top of the bell tower were ruined, and the bells were removed, with the roof deteriorating.

The brick two-story church consists of a tall slender square base, a short refectory, and a bell tower. The upper church is two-light, with rich moldings in the shape of rooster combs on the second tier and simpler triangular pediments on the third tier, which were likely removed during the 19th-century reconstruction. A four-pitched roof covers a row of small kokoshniks. There is one dome, although it is assumed that there could have originally been five. The bell tower, built in the classical style, was constructed in the first third of the 19th century. The first two tiers of the bell tower are square, with an unusual design on the second tier: in the center of each side wall is a niche surrounded by radiating rustication, with a vase inside. The ringing tier is cylindrical, decorated with paired columns of the Tuscan order at the corners of the square.

In the church, in addition to the main altar of St. Nicholas the Wonderworker, the Three Saints, All Saints, Introduction, and Kirillo-Novozeretsky chapels were consecrated. The altar part is two-apsidal, which is uncharacteristic for Russian architecture in general but common in Vologda.

St. Petersburg art historian and architectural critic G. K. Lukomsky described the interiors of the church in the early 20th century as follows: "Above the entrance to the church is an ancient icon in a silver setting. The iconostasis is beautiful, consisting of two semicircles. In the upper church, there is a lovely iconostasis with columns and high pediments. However, all the frescoes in the church are terrible. The chandelier is beautiful, not ancient, but of excellent design."