The first church lost to the Great Fire was St. Margaret New Fish Street; it was not rebuilt, the parish being united with St. Magnus and the site given to The Monument, which stands 202 feet to the east of the spot where the fire began. In 1831, St. Michael Crooked Lane (also rebuilt by Wren after the Great Fire), fell to another great destroyer of City churches, urban redevelopment, being demolished to make way for King William Street during the rebuilding of London Bridge. The parish was united with that of St. Magnus, and was one of 51 parish churches rebuilt by Sir Christopher Wren and his office after the Great Fire (in fact, the enterprising parishioners had already begun to rebuild the north wall with the mason George Dowswell by 1668). The work spanned 1671-84, but was substantially complete by 1676; at £9579 19s 10d, it was one of his most expensive churches. Wren’s craftsmen were John Thompson, mason; Matthew Banckes Senior and Thomas Lock, carpenters; William Cleere, joiner; Doogood & Grove, plasterers; with internal woodwork by William Grey and one Massey. Although the model for the steeple was probably made by 1684 (very closely based on that of St. Charles Borromée by François Aiguillon in Antwerp), it was only completed in 1703-06.
Rebuilding after the fire of 1760 coincided with the last major renovation of old London Bridge, which saw the demolition of its shops and houses, and the expansion of pedestrian access literally through the west end of the church: two of its nine bays were demolished, and the tower base converted to an external porch pierced by arches to create a path between Fish Street Hill and the bridge (possibly to designs by George Dance the Elder, the City Surveyor). The building now stands 90ft (27m) long, 59ft (18m) wide and 41ft (12.5m) high, with a 185ft (56m) steeple.