The church was medieval in origin, and Stow traced its roots back to 1266. By 1606, it had fallen into a ruinous state and had to be propped up. It was subsequently demolished and rebuilt. The patronage of the church was with the Prior and convent of St Mary Overie, Southwark, then, after the dissolution, with the dean and chapter of Canterbury Cathedral.
In 1670 a Rebuilding Act was passed and a committee set up under the stewardship of Sir Christopher Wren to decide which would be rebuilt after the Great Fire. Fifty-one were chosen, but Holy Trinity the Less was one of the minority never to be rebuilt.
After the fire, the church's parish was united with St Michael Queenhithe, The site of the burnt out Anglican church was used for a German Lutheran church, which opened in 1673. It survived until 1871 when it was closed and demolished to make way for the Mansion House underground station The churchyard was razed in 1872 to make room for the station.
^"The City of London Churches" Betjeman, J. Andover, Pitkin, 1967 (rpnt 1992) ISBN 0-85372-565-9
^A separate churchwarden was appointed for former Holy Trinity worshippers Church of England, Parish of St. Michael Queenhithe. - Rough registers of baptisms, marriages and burials, 1694. - M0013822CL. - M0003091CL cited in "City of London Parish Registers Guide 4" Hallows,A.(Ed) : London, Guildhall Library Research, 1974 ISBN 0-900422-30-0