The history of this gate church is connected with three notable figures. The first is Empress Elizabeth Petrovna, daughter of Peter the Great. In September 1742, she unexpectedly visited the Zlatooustov Monastery, which was still recovering from the fire of 1737 and was in a deplorable state. Passing through the holy gates, the empress noticed that the Protection Church above them was almost destroyed. The visit coincided with the feast day of Prophet Zacharias and Righteous Elizabeth, the heavenly patrons of the empress, and she allocated 2000 rubles for the construction of a new gate church in their honor. The church, built in the Moscow Baroque style, was erected quickly and consecrated on December 18, 1742, by Bishop Lev, the former bishop of Voronezh.

Bishop Lev was a symbol of resistance to the 'Bironshchina' in the 1730s-1740s, for which he was stripped of his rank and spent 10 years in exile. With the ascension of Elizabeth Petrovna to the throne, he was restored to the episcopal rank, and she took him under her patronage, which explains why he consecrated the church founded by the empress.

The third figure associated with the Church of Zacharias and Elizabeth is architect I.F. Michurin. Some historians believe he is the author of the church, noting stylistic similarities with his other works, although there is no direct evidence for this. It is known that Michurin was well acquainted with the Zlatooustov Monastery: in 1756, he described its dilapidation and prepared estimates for new constructions.

In 1933, the Church of Zacharias and Elizabeth was destroyed. The A.V. Shchusev Museum of Architecture holds photographs of its exterior and interior decoration taken in the last years of its existence: the iconostasis, the gallery grille, the small chandelier. The small and large chandeliers that illuminated the Trinity Church of the Zlatooust Monastery were military trophies of Admiral Count F.M. Apraksin, obtained during the Northern War. They were kept at his home as symbols of the victories of the young Russian fleet, to which Apraksin dedicated his life. After his death, his heirs donated the lamps to the Zlatooust Monastery in his memory. The chandeliers remained there for 200 years, and in 1929 were purchased by the Finnish envoy, returned to their historical homeland, and are now in the museum of the city of Vaasa in Finland. Theoretically, the Church of Saints Zacharias and Elizabeth could also be restored in Moscow: the A.V. Shchusev Museum holds measurements of it from the 19th century, allowing it to be recreated in its original form.