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The name St. Mary de Lode, the church in St. Mary's Square, is an indication of the proximity of a now extinct channel of the River Severn, the word lode meaning a passage across a river. This name is first recorded in 1523, the church having been previously known as St. Mary before the abbey gate. The church is the elder of the area, with a history to rival that of the Cathedral.

The church first appears in the documentary record in the mid-12th century, though a mention of the only parish church in Gloucester that appears in the Domesday Book of 1086 is believed to be a reference to St. Mary de Lode.

The tower (minus its spire, probably a victim of storms in 1703) and chancel (the part of the church closest to the Cathedral) date to 1190. A complete rebuild of the nave in 1826, however, uncovered Roman archaeological remains which reveal the site has been built upon since the early days of the Roman period at Gloucester.

The archaeological record begins with a Roman building of high status dating to the late-1st or early-2nd century. This was replaced sometime from the mid-2nd century with a Roman temple or baths complex, with the evidence favouring the latter interpretation. The building comprised a range of rooms arranged around three sides of a central space. The walls show signs of being painted over several phases, the first of which showed a high quality. One of the rooms was built over a hypocaust, the Roman system of underfloor heating. At some date unknown, the building was at least partially destroyed by fire and was later levelled.

In the post-Roman period there is evidence in the archaeological record of a 5th- or 6th-century Romano-British timber building and burials which can be interpreted as an earlier religious site, leading to speculation that the site was the location of Britain's first Christian church, one that pre-dated the Saxon period. There is a tradition that the site is the final resting place of Lucius, a legendary 2nd-century king of the Britons credited with introducing Christianity to Britain, though this is not accepted in scholarly sources. The Romano-British building was replaced by a Saxon church, the archaeological evidence for which dates it to the 10th or 11th centuries, after the Roman colony of Glevum had been resurrected as Gloucester, an important stronghold in in the Saxon kingdom of Mercia.

At the beginning of the Norman period, when the first stones of today's Cathedral were laid, St. Mary de Lode served as the parish church for the abbey's extensive lands in and around Gloucester. The parish included Tuffley, much of Barton Street and Wotton, and parts of Kingsholm, Longford and Twigworth. Furthermore, the churches of Maisemore, Barnwood, and Upton St. Leonards were subject to St. Mary's.

The church was once surrounded by a graveyard. St. Mary's received burial rights as far back as the late Anglo-Saxon period, and by c.1100, when Gloucester boasted ten churches, it was one of only three to hold the right of baptism and burial, alongside the abbey and St. Oswald's. An open space between graveyard and St. Mary's Gate, known in the 19th century as the Knapp, was where John Hooper, the Protestant former Bishop of Gloucester was burned at the stake in 1555 on the orders of the Catholic Queen Mary I.

The church was twice used during the English Civil War to detain Royalist prisoners, in 1643 during the siege of Gloucester, and again in 1646.

A 12th-century abbey lease and maps of 1610 and 1712 show that properties have long existed around church and graveyard, among them two alehouses shown in 1712 in the western part of the yard which were demolished in 1861. The graveyard was used until 1854, and gravestones could still be seen in the 1930s.

In the mid-20th century, post-war redevelopment altered the square considerably. Old buildings were replaced by modern housing, gravestones were removed and the occupants of the plots they marked reinterred elsewhere. It's almost certain that numerous unmarked burials still lie in the former graveyard which, with the exception of a statue opposite St. Mary's Gate commemorating the martyring in 1555 of Bishop John Hooper, was sold in 1956 to Gloucester City Council.