Trinity Church in Vishnyaki is first mentioned in 1642 as a wooden structure in the streltsy settlement. In 1678, the streltsy from the "Matveevsky Order of Vishnyakov" rebuilt it in stone in memory of their comrades who died during the siege of Chigirin. The alley where the church stands was previously called Luzhnikovsky (or Luzhnetsky), but in 1922 it was renamed Vishnyakovsky to avoid duplication with Moscow streets.

The fate of Matvey Mikhailovich Vishnyakov, the head of the streltsy, was tragic. During the streltsy uprising of 1682, he was dismissed and then arrested along with his father, deacon Mikhail Vishnyakov. Both were tortured, and the father died, while Matvey was tonsured as a monk and exiled. His further fate is unknown.

In the early 19th century, the church was completely rebuilt with funds from merchant Semyon Loginovich Lepyoshkin, whose estate was located opposite. Lepyoshkin was a first-guild merchant, a councilor of commerce, a hereditary honorary citizen, and served as Moscow's mayor from 1846 to 1849. During his time, the Moscow Merchant Society created a fund to buy bread in years of poor harvest, collected donations for the illumination of Red Square and the Gostiny Dvor for the 700th anniversary of Moscow, and established a hospital in case of a cholera epidemic. The church was ready for consecration, but due to Napoleon's invasion, it was not consecrated in time, and after the French left, the church had to be repaired.

In 1826, a new bell tower in the classical style was added to the church. At the end of the 19th century, the church was renovated. The ringing of the bells of the Trinity Church made a strong impression on the famous bell ringer K. K. Saradjev in his childhood and influenced his fate.

In 1922, the church, like other Moscow churches, was looted by the new authorities, and a significant amount of gold and silver items was confiscated. Soon the church was closed, the clergy's house and pavilion were demolished. Various offices were located in the building, and in the 1980s, it housed the personnel department of the "Moscow Design Technical Bureau." In 1991, the church was the first in Zamoskvorechye to be returned to the faithful. Today it serves as a church for the Orthodox Saint Tikhon Humanitarian University, where faculty and students of the church arts department work on interior design. The altar features a mosaic made of smalt in the Byzantine classical style.