The massive and majestic building of the church rises above all surrounding structures. Even the modern construction of the 20th century could not overshadow it or diminish its significance in shaping the appearance of New Square. However, the crosses on the church and bell tower have only recently reappeared.

The exact date of the construction of the first church is unknown, but it is mentioned as early as 1493. It next appears in sources nearly a century later, in 1585, as a wooden structure. At that time, its nickname 'Under the Elm' became known, due to the large tree that grew near the altar until 1775. By the early 19th century, the old church building had fallen into disrepair, but reconstruction was postponed due to the Patriotic War of 1812. Only in 1825, a date still visible on the pediment above the altar, did construction begin based on the designs of architects S.P. Obitaev and L.P. Karloni, which lasted 12 years and was completed in 1837.

Built in the Empire style, the two-tiered building of the new church received six altars, which was a significant number for a parish church. At the top, the main altar is dedicated to St. John the Theologian, with two chapels: the Finding of the Head of John the Baptist and Evangelist Luke. Below, the central chapel is dedicated to the Protection of the Holy Virgin, with side chapels for St. Nicholas the Wonderworker and Mitrophan of Voronezh. The church faces New Square with its eastern facade featuring an altar designed as a massive six-column portico with rustication at the lower part and no projections. The side facades are decorated more modestly. A high light dome adorned with Ionic columns and topped with a traditional Orthodox church cupola adds special solemnity to the building. In the 1840s, the church received a new bell tower, nearly matching the height of the church dome thanks to an elongated spire with a cross. Symmetrically located on the north and south sides of the church are two-story Empire-style houses of the clergy with shops on the first floor: connected to the church by arched gates with ornate finishes, they form a complete ensemble with it.

In 1925, the church was closed, one of the first in the area, and was initially used as an archive, then as a communal museum, which in 1934 became the Museum of the History and Reconstruction of Moscow. The church lost its cupola and the bell tower spire, interior floors were added, and almost all decoration was destroyed, except for some fragments of stucco. Until the museum moved to the Provianthouses building on Zubovsky Boulevard, the church remained closed. Only in 2011 did services resume here, and the church received the status of a house church at the Russian Orthodox University of St. John the Theologian. Restoration work was carried out, during which the lost finishes of the church and bell tower were recreated, and there are plans to restore the lost appearance of the interiors. The work was completed as part of the subprogram 'State Protection, Preservation, and Promotion of Cultural Heritage Sites' of the State Program of the City of Moscow 'Culture of Moscow for 2012-2019.'