The church here was first established as a chapel of ease of St Dunstan's Stepney, becoming a separate parish in 1669 and consecrated as St Paul's Shadwell in 1671.
It became known as the church of Sea Captains due to the many mariners in the congregation, including Captain James Cook, whose marriage banns to Elizabeth Batts were read in the church and whose son, also James, was baptised here in 1763. The maritime trade led to Shadwell being a point of arrival for immigrants such as the Huguenots in the 17th century and a mulberry tree in the rectory garden may have been planted for their silk industry. In 1811 the church was closed as it was in danger of collapse and the parishioners then petitioned for a new church.
By this time the local population mainly worked in the docks or on the Thames. The petition was successful and in 1820 the church was substantially rebuilt as a Waterloo Church by the architect John Walters and builder R Streatham, which is recorded on a plaque on the church.
It was once surrounded by trees on all four sides but in the 1840s part of the churchyard was compulsorily purchased when the London Dock Company built Shadwell New Basin.
After it closed for burials, the churchyard was laid out in 1886 as a public garden by the MPGA, with a partially flagged area in front.