In 1627 the East India Company (EIC) purchased a house in Poplar High Street to be used as a hospital for disabled seamen.

In 1633 the inhabitants of Poplar and Blackwall – largely employees of the EIC – requested that a chapel be built there as St Dunstan's, Stepney was too far away for them.

When Gilbert Dethick, the Lord of the Manor of Poplar, died in 1639 he left a further £100 towards the building of the chapel, on the condition that work started within three years of his death.

This gives a Dutch flavour to the architecture reminiscent of Hendrick de Keyser who built several churches in Amsterdam in the early seventeenth century.During the eighteenth century various changes were made: a tower added (1718), a triple-decker pulpit (1733) and extensive repairs and alterations to the windows in 1775–1776 (architect: Richard Jupp).

In the early 19th century a mural monument to George Steevens by John Flaxman was commissioned; this is currently on loan to the Fitzwilliam Museum, Cambridge.

Stained glass windows incorporating masonic imagery were installed in 1920 by East London lodges as a memorial to their brethren who had died in the First World War.

The UK agents of the overseas purchaser, Cheval, refused to accept the 'Arts Centre' and demanded local involvement in determining future use as well as the establishment of a "sinking fund" to maintain St Matthias in perpetuity.