The church (as a chapel of ease) was licensed by bishop Ralph Baldock of London on 17 November 1311 for the people of Stratford-at-Bow within the parish of Stepney.

Before this, local people were obliged to travel to St Dunstan's, Stepney, to attend church.

The chapel of ease allowed them to practise their religion locally, but they were still obliged to attend St Dunstan's at Stepney on religious holidays and to pay for its upkeep.

In 1497, following a dispute about the terms of this arrangement, an agreement was then reached, whereby the people of Bow promised to acknowledge themselves as parishioners of Stepney and agreed to pay 24 shillings annually for repairs of the mother church, and to dispense with their attendance there, except on the feast of Saint Dunstan, and on the Wednesday in Whitsunweek, when they were to accompany the rest of the parishioners in procession to Saint Paul's Cathedral.

In 1767, the church became the resting place of colonel Philip Ludwell III, the earliest known convert to Eastern Orthodoxy in America.

In 1896, the chancel roof collapsed, prompting a major restoration by the architect Osborn C Hills.

The site was visited by Queen Elizabeth in 1951 to mark the start of a campaign to restore the church, the work was overseen by the architect H S Goodhart-Rendel.