Up until the early 14th century the church served the whole of Middlesex east of the City of London. Then new churches were built at Whitechapel and Bow. The existing building is the third on the site and was built of Kentish ragstone mainly in the 15th century (although the chancel dates from 200 years earlier). A porch and octagonal parish room were added in 1872.
The ring of ten bells, the heaviest weighing 28¾ hundredweight, which hang in the belfry were cast at the local Whitechapel Bell Foundry and are tuned to C#. The seven oldest bells were cast by Thomas Mears and Son, Whitechapel, in 1806. Three were recast in 1952 when repairs were made to the tower. The bells are mentioned in the nursery rhyme Oranges and Lemons "When will that be, say the bells of Stepney".
The church is surrounded by a churchyard of nearly seven acres (28,000 m²). In 1658 William Greenhill was appointed vicar whilst retaining his position as a preacher at Stepney Meeting House. He held this post for about seven years, till he was ejected immediately after the Restoration in 1660.
Shortly after this, the churchyard was enlarged to cope with the massive number of deaths during the Great Plague of London. In one eighteen month period 6,583 died, with 154 being buried in one day in September 1665.
The church has a long traditional link with the sea and many sailors were buried here. It was once known as the 'Church of the High Seas'. The graveyard is also where Roger Crab the 17th-century hermit is buried after living on a diet solely of herbs, roots, leaves, grass and water.
The Church continues to be open to visitors and worshippers from all over the world. There is an active congregation who help to continue the life of the church community. As well as the Arbour Centre (a St Dunstan's community project) there is a close connection with two schools; Stepney Greencoat Church of England Primary School and Sir John Cass and Redcoat Church of England Secondary School. St Dunstan's also employs a Children and Community Worker funded by the Bishop of London's Mission Fund.