Holy Trinity, Minories, was an Anglican parish church outside the eastern boundaries of the City of London; but within the Liberties of the Tower of London. The liberty was incorporated in the Metropolitan Borough of Stepney in 1899, and today is within the City of London. Converted from the chapel of a nunnery, Holy Trinity was in use from the 16th century until the end of the 19th century.
The parish covered an area previously occupied by the precincts of a convent of St Clare, founded by Edmund Crouchback, in 1293, for a group of Spanish nuns of the Order of St. Clare who arrived with his wife. The nuns were also known as the Minoresses – which came to be adapted as the name for the district, Minories. The nunnery was surrendered to the Crown in 1539, during the Dissolution of the Monasteries, and the buildings, excluding the chapel, were used as an armory for the Tower of London, and later, as a workhouse. Some of the abbey buildings survived until their destruction by fire in 1797.
The nuns' chapel became a parish church. Considerable changes were made to the building: all the ancient monuments were removed, a gallery, a new pulpit and pews were installed, and a steeple was built. The first recorded reference to a dedication to the Holy Trinity dates from 1563. Later in the 16th century, the church was a Puritan stronghold, where both John Field and Thomas Wilcox preached. Until 1730, the church claimed the rights of a royal peculiar – including freedom from the authority of the Bishop of London; and the right to perform marriages "without licence".
The church escaped the Great Fire of London but fell into disrepair and was rebuilt in brick in 1706, retaining the north wall of the medieval building. The new church was a plain structure, a single space undivided by pillars or columns, 63 feet (19 m) long and 20 feet (6.1 m) wide, built at a cost of £700. The bells were housed in a wooden turret above the projecting porch.