The medieval church building had a nave, a chancel, a south porch and a northwest tower, which was rebuilt in 1534 using rubble masonry containing Roman bricks, finished with limestone dressings,[2] which included a frieze of shields around the base, still visible today.

[7] The rectors of St Mary's appear to have supported the Protestant Reformation; records show that they sold off the church's silver-gilt pyx and other accoutrements in 1534 and removed stained glass windows in 1548.

[8] The Royalist defenders established an artillery battery in St Mary's churchyard to fire over the town wall, directed by observers on top of the church bell tower.

Under the command of a one-eyed master gunner called Thompson, they hoisted a brass saker (a small cannon firing a 5.25 pounds (2.38 kg) ball) into St Mary's tower, where it was mounted on a platform built over the bell-frames.

The new building, consisting of a small chancel, a nave with aisles and a west gallery,[2] was described by local antiquarian Philip Morant as "plain, neat... but not so substantial as others of its kind".

[14] At the same time, the ancient "low and inconvenient" postern gate in the Roman wall which gave access to the churchyard was enlarged and stone steps were added.

[15] The tower was still a ruin in 1722 when Daniel Defoe visited the town,[16] but it was finally repaired in brick in 1729, although plans to surmount it with a cupola and stone pineapples came to nothing,[2] the rather plain result being described by Morant as "both heavy and ugly as possible".

Starting in 1872, a new chancel and south chapel were built first, and then the rest of the old church buildings, except the tower, were demolished and rebuilt in red and black brick to the design of Arthur Blomfield.

The upper part of the tower, which was damaged in the 1884 Colchester earthquake, was rebuilt in 1911, along with the addition of new choir stalls and the cladding of Blomfield's cast iron columns in terra cotta.

[20] A focus on emerging talent has resulted in early performances by bands including Coldplay, The Libertines, Ash, The Killers, and The Strokes and comedians Eddie Izzard, Graham Norton, Harry Hill, Catherine Tate, Jo Brand, Bill Bailey, and Jack Dee.