The body of the medieval church was destroyed in the Great Fire of London of 1666, and was replaced with a new structure by the office of Sir Christopher Wren.

From its situation in the quarter of London inhabited by many Jews, John Stow asserted, incorrectly, that the building had been used as a synagogue.

The Dean and Chapter of St Paul's put in counter-claims, but the matter was resolved in Butley's favour in 1452.

In 1431, John Sokelyng, who owned a neighbouring brewery called 'La Cokke on the hoop', died and left a bequest to St. Stephen's on the condition that Mass be sung on the anniversary of his death and that of his two wives.

[7] The gift was commemorated by a cock in a hoop motif that would decorate the church until 1940 and can still be seen in parish boundary markers.

Finding Boston torn by religious dissent they diverted to Long Island Sound, where they founded the plantation of New Haven Colony, Connecticut.

[14][15] Dame Margaret Wroth, a patron sympathetic to his views, who died in 1635 and was buried here beside her husband's parents, left benefactions for sermons to be preached on the anniversaries of her own burial and that of her daughter.

[16] Goodwin was ejected from St Stephen's in 1645 for setting up a covenanted community within his parish and was briefly imprisoned after the Restoration for his political views.

The walls of the medieval tower quite substantially survived the Fire, and their old masonry remained visible on the north side in the later building, refaced with Portland Stone towards the top.

Wren's church retained the plan of its medieval predecessor, which was in the form of an irregular quadrilateral that tapered towards the east.

The main façade, at the east end, towards Coleman Street, was faced with Portland stone with rusticated corners, and had a circular pediment between two pineapples.