The monument does not have a chronicle date. The Trinity Church is first mentioned in 1571 in connection with the wedding of Tsarevich Ivan Ivanovich. From the late 1560s until 1582, the priest of the cathedral was the famous composer of Ivan the Terrible's era, Fyodor Krystyanin.

After the Polish-Lithuanian intervention, it was one of four churches that suffered at the Tsar's court. In 1641, the vacant church was repaired and consecrated, and new "royal chambers," the wooden part of the palace, were built nearby. In 1680, the Trinity Church was rebuilt into a larger monastery refectory church.

A two-pillar chamber with a tent bell tower was added to the western side; the church tent was supplemented with an octagonal dome vault, the altars were expanded, and a new chapel of Fyodor Stratilat appeared at the southeast corner, replacing the old one at the northeast corner. After the construction was completed, the Trinity Church was reconsecrated: its altar was moved to the neighboring Pokrovskaya Church (now the Trinity Cathedral), and the cathedral's altar was moved to the Trinity Church.

Until the 1990s, the dating of the tented Trinity Church was attributed to the second construction period of Sloboda, the time of Ivan IV (from 1565 to 1582). Construction could have begun before the arrival of Grozny, so the 1560s or 1570s were tentatively accepted. The basis for this dating was its tented top, as the first tented church was considered to be the Ascension Church in Kolomenskoye, built in 1529-1532. On this basis, the Trinity Church could not be dated to the first construction period of Sloboda, the 1510s (the time of Vasily III).

This dating was maintained until the research of V. V. Kavelmakher. In the 1980s and 1990s, he conducted extensive excavations and soundings, revealing that the Pokrovsky Cathedral, Trinity Church, Assumption Church, and the Church of Metropolitan Alexius (now the Crucifixion Bell Tower) in Alexandrov Sloboda were built in the same construction period, the 1510s. This was confirmed by further research by S. V. Zagraevsky, Kavelmakher's son. However, this version has not yet been recognized by other authoritative researchers.

Thus, it can be assumed that the Trinity Church was built by Vasily III in his residence, which was later inherited by Ivan the Terrible.

According to one hypothesis, it was in the Pokrovskaya Church that one of the first known Russian composers, Fyodor Krystyanin, served as a singer.

In the 17th century, the temple became surrounded by new buildings and was somewhat "drowned" among them. Among the additions was a four-sided tent bell tower with a clock that measured time by the rising and setting of the sun. Fragments of the ancient clock mechanism are kept in the local museum.

In the 18th and 19th centuries, the former court church underwent numerous changes that distorted its original appearance. The northern wall had deep cracks and deformations. A comprehensive restoration was carried out in 1960-64, during which the four-pitched roof of the refectory and the lathing covering of the tent were restored.

In the 16th century, the temple was painted. The frescoes have mostly survived in the tent, with fragments found in the middle apse and on the slopes of the western window. In 1863, at the initiative of merchant Zorina, the ancient painting was replaced with new ones, and the iconostasis was also replaced.

The Trinity Church belongs to the type of tented churches, close to the traditional, with three apses and a square base, topped with a horizontal tie, with kokoshniks on the edges of the octagon. The ancient core of the church includes the church itself, a double white stone undercroft, and a sacristy. Under the undercroft are two deep cellars. All rooms, arranged in three floors starting from the cellars, have transverse orientation and a slightly elongated plan. The main facade of the building, the southern one, faced the center of Vasily III's palace.

The church and the chamber represent a combination of two interpenetrating volumes of different heights and configurations. The church square stands on a high white stone plinth and is crowned with a white stone cornice of original profile. The square and the tent are decorated with brick arches and recesses.

The Trinity Church is built of oversized bricks and white stone on oak and metal ties, on high-quality lime mortar. The masonry is mixed, and from tier to tier, the volume of white stone decreases. In the third tier, only the sacristy and three altar apses are fully laid out in white stone. Brick predominates in the decoration of the church and chapel. The bases, pilasters, and portals (not fully) are made of white stone, as well as the structural elements of the cornices and kokoshniks, and they are also faced to half the height of the walls in the interior. The upper parts of the building are almost entirely brick.

The white stone portals of the temple were made by a foreign artist. The southern and northern portals, as well as the portal of the chapel of Fyodor Stratilat, are gabled; the western one has a semicircular top. A unique feature of 16th-century architecture, the arcosolium under the western wall, may be the burial place of a member of the royal family.