The Church of St Mary Magdalen's may have been founded by Eudes the sewer in the 12th century as the chapel of St Mary Magdalen's Hospital, but it had acquired parochial status by 1237 when the church ecclesia, of St Mary Magdalen was confirmed to St John's Abbey, and in 1254 the master of the hospital was rector of the church.

The medieval church of St Mary Magdalen stood on the north side of Magdalen Green, north of the modern Magdalen Street. It seems to have compromised an aisleless nave and chancel with an adjoining chapel for the lepers. The nave contained a 13th century south doorway and windows of the 14th and 15th centuries. A porch of unknown date survived in 1601. The hospital chapel had been destroyed before 1610 and the church needed repair in 1633. After the siege in 1648 it was abandoned until 1721 when Thomas Parker, the Lord Chancellor, repaired it at his own expense. The 18th century church comprised a small brick chancel, presumably built in 1721, and the repaired medieval nave. The church was demolished on 1852 and a new one built on the site.<1>

The church is shown on Norden's / Speeds's map of 1610.<2>

The Museum holds a print of a painting of St Mary Magdalen's Church from 1783 , the view faces north. <3>

Excavations in 1989 uncovered the site of the Medieval Church in the graveyard of the later Victorian Church (Colchester Building 185). The excavations revealed the nave, chancel and porch of the church. The walls of the nave rest on c.12th century foundations composed of alternating layers of light clay and compacted mortar, a distinctive constructional technique found on several of Colchester's monastic sites. With such early origins it seems likely that the building was originally laid out as a chapel for the hospital, then converted to a church upon the formation of the parish of St Mary Magdalen in the early 13th century.<4><6>

A grave was found under the church floor containing the remains of a man with a pewter chalice laid on his chest, a strong indication that this was an early master of the hospital. Notable architectural finds from the church included a variety of stonework ranging in date from the 12th to the 15th centuries; also found was nearly a hundred pieces of late medieval decorated floor tile.<5>