For many years St Leonard's served as the church of the port of Colchester.[2] Its earliest fabric dates from the 14th century. Additions and alterations were made in the following century, and the hammerbeam roof of the nave dates from the early 16th century.[1] During the Siege of Colchester in the Civil War, Royalist soldiers took refuge in the church.[4] Bullet holes from this incident survive in the door.[2][4] In the earthquake of 1884 the tower was damaged and its top stage was replaced.[1]
The screens and furnishings date from the 19th and 20th centuries. Over the chancel arch is a mural dated 1901. Stained glass windows depict various saints.[2] Over the centuries the church has required repeated restoration due to subsidence, or to inadequacies in the earlier construction.[1]