There was originally a Saxon church here and since 1286, three different churches have stood on this location, with the nave and chancel of the current building dating from 1872. The lower part of the tower is the oldest, dating from around 1270. The city wall forms the west side of the churchyard.
During the reign of Queen Mary on 2nd August 1557, six Protestants were burnt at the stake next to the church by the city wall. Colchester saw more burnings than any place in England outside of London, probably because there were so many Protestants here.
During the Civil War Siege of Colchester in 1648 when Royalist forces occupied the town and defended it against and encircling force of Parliamentarians, an allegedly one-eyed Royalist gunner named Thompson hauled his 'saker' (a small cannon) to the top of the tower of St Mary's church. He was a very accurate shot and the vantage point allowed him to direct damaging fire onto the besieging troops under the command of Lord Fairfax.
On the morning of 14th July 1648 shortly after six o’clock, the Parliamentary gunners concentrated their fire on St Mary's tower, and eventually hit the unfortunate Thompson and sent the gunner and his weapon falling to the ground. Some will say that this is the origin of the nursery rhyme “Humpty Dumpty”, but there is no truth in this.
The damage caused by the Parliamentary guns is evident. When the tower was finally repaired in 1750, the builders used red brick, which stands out clearly from the reused Roman materials in the lower part of the tower. The ramparts at the top of tower date from the rebuild of 1911 as the top came loose during the Essex earthquake of 1884.
In 1882 the Reverend John Irvine was Rector of the church. He was concerned that the Balkerne Hill Water Tower, which was being built at the time, would be 16 feet from his rectory which stood where the Mercury Theatre is. He wrote to local paper describing it as a Jumbo because in 1882 London Zoo sold an elephant called Jumbo to P.T. Barnum’s circus. Jumbo's sale caused a great uproar throughout England, with Queen Victoria and the Prince of Wales amongst those concerned. In honour of this great elephant the local people gave the nickname to the water tower. The council placed a gilt weathervane in shape of an elephant on top. It has pink eyes and is still there.
There were two other notable rectors. The first from 1737 to 1773, was Philip Morant, a historian and author who wrote “The History and Antiquities of Colchester” and “History and Antiquities of the county of Essex” between 1763 and 1768. The second from 1788 until 1804, was Thomas Twining, He was the grandson of Thomas Twining the tea merchant who formed the Twining Tea Company.
The church finally closed for worship on 26th February 1978. The congregation moved to Christ Church in Ireton Road. In 1980, St. Marys then became the Colchester Arts Centre which is a venue for entertainment from live music to comedy events.