The wooden church in honor of the Holy Trinity is believed by researchers to have existed as early as the 16th century, but it is first mentioned in sources in 1620. In the same century, the State Money Chamber was established here, where silver coins were minted. Surrounding it lived craftsmen known as silverworkers, who were the main parishioners of the Trinity Church and gave it the name "in Serebryaniki." On the map of Moscow, this settlement is represented by the Serebryanicheskaya embankment of the Yauza River and a street of the same name, where the church stands. By 1657, the church was already made of stone, but it was expanded several times later. In 1764 and 1768, with the funds of Afanasy Goncharov, whose estate near the church has survived to this day, the existing bell tower was built. In 1781, the wife of a merchant of the 1st guild, Tatyana Surovshchikova, donated funds for a new church, which was erected on a basement using part of the old walls.

It is believed that the bell tower was designed by architect K.I. Blank, the author of the Educational House nearby. This is one of the last examples of baroque in church architecture in Moscow. The bluish color with white details, cartouches and rocaille, paired columns, decor of arches and capitals with cherub figures, all this is characteristic of baroque. The first tier is decorated with rustication, indicating the influence of classicism. The bell tower of the Trinity Church in Serebryaniki resembles the bell tower of the Nikolsky Marine Cathedral in St. Petersburg, especially in color scheme and details, although the latter is more elegant. Afanasy Goncharov, the owner of a neighboring factory, arranged a church in the first tier of the bell tower in honor of the Beheading of John the Baptist for the commemoration of his parents. In the main church, after reconstruction, chapels were created in honor of the Kazan Icon of the Mother of God and St. Basil the Great, the latter of which was established by merchant Vasily Surovshchikov. The main part of the church is not connected to the bell tower and represents a separate building with elements of classicism: pilaster porticos and an elongated refectory. The completion of the church is made in the form of a cube with truncated corners, on the faces of which are oval windows and stucco depicting a cross, the Gospel, an epitrachelion, and a censer.

After the revolution, the church was closed and used as housing, then for offices, and later became a warehouse for the "Diafilm" studio. Due to the rising level of Yauza Street in front of the Astakhovsky Bridge, the first tier of neighboring houses and part of the lower tier of the bell tower were hidden by new embankments, distorting the historical view of the Trinity Church. Since 1993, the complex has been returned to the faithful, but during the restoration, services were only held in the chapel of the bell tower. It was not until 2001 that the first liturgy was held in the main part of the church.