Archaeological evidence suggests that the area of London Bridge head was not occupied from the early 5th century until the early 10th century.

Environmental evidence indicates that the area was waste ground during this period, colonised by elder and nettles. Following Alfred’s decision to reoccupy the walled area of London in 886, new harbours were established at Queenhithe and Billingsgate. A bridge was in place by the early 11th century, a factor which would have encouraged the occupation of the bridgehead by craftsmen and traders.

St Magnus was built to the south of Thames Street to serve the growing population of the bridgehead area and was certainly in existence by 1128-33.

Until 1831, London Bridge was aligned with Fish Street Hill, so the main entrance into the City from the south passed the West door of St Magnus on the north bank of the river. The bridge included a chapel dedicated to St Thomas Becket for the use of pilgrims journeying to Canterbury Cathedral to visit his tomb. The chapel and about two thirds of the bridge were in the parish of St Magnus. The church jutted into the road running to the bridge and it grew in importance.

St Magnus Corner at the north end of London Bridge was an important meeting place in mediaeval London, where notices were exhibited, proclamations read out and wrongdoers punished. As it was conveniently close to the River Thames, the church was chosen by the Bishop between the 15th and 17th centuries as a convenient venue for general meetings of the clergy in his diocese.

The church had a series of distinguished rectors including Myles Coverdale (Rector 1564-66) who oversaw the production of the first complete bible in the English language.

St Magnus narrowly escaped destruction in 1633 in a fire that burned many buildings upon London Bridge but, despite this, the church was one of the first buildings to be destroyed in the Great Fire of London in 1666. St Magnus stood less than 300 yards from the bakehouse of Thomas Farriner in Pudding Lane where the fire started. Farriner, a former churchwarden of St Magnus, was buried in the middle aisle of the church on 11 December 1670, perhaps within a temporary structure erected for holding services.

The parish engaged the master mason George Dowdeswell to start the work of rebuilding in 1668. The work was carried forward between 1671 and 1687 under the direction of Sir Christopher Wren, the body of the church being substantially complete by 1676. At a cost of £9579 19s 10d, St Magnus was one of Wren’s most expensive churches.

Shortly before his death in 1711, Sir Charles Duncombe, Alderman for the Ward of Bridge Within and, in 1708/09, Lord Mayor of London, commissioned an organ for the church, the first to have a swell-box, by Abraham Jordan (father and son). A swell organ uses pipes set apart in a box which can be opened or closed to alter the volume. The organ case, which remains in its original state, is looked upon as one of the finest existing examples of the Grinling Gibbons’s school of wood carving.

Canaletto drew St Magnus and old London Bridge as they appeared in the late 1740s. Between 1756 and 1762, under the London Bridge Improvement Act of 1756, the Corporation of London demolished the buildings on London Bridge to widen the roadway, ease traffic congestion and improve safety for pedestrians.

As part of the bridge improvements, overseen by the architect Sir Robert Taylor, a new pedestrian walkway was built along the eastern side of the bridge. With the other buildings gone St Magnus blocked the new walkway. As a consequence it was necessary in 1762 to 1763 to remove the vestry rooms at the West end of the church and open up the side arches of the tower so that people could pass underneath the tower. The tower’s lower storey thus became an external porch.

By 1782 the noise level from the activities of Billingsgate Fish Market had become unbearable and the large windows on the north side of the church were blocked up leaving only circular windows high up in the wall.

In 1823 royal assent was given to ‘An Act for the Rebuilding of London Bridge’ and in 1825 John Garratt, Lord Mayor and Alderman of the Ward of Bridge Within, laid the first stone of the new London Bridge. In 1831 Sir John Rennie’s new bridge was opened further upstream and the old bridge demolished. St Magnus ceased to be the gateway to London as it had been for over 600 years.

Until 1922 the annual Fish Harvest Festival was celebrated at St Magnus. The service moved in 1923 to St Dunstan in the East, but St Magnus retained close links with the local fish merchants until the closure of old Billingsgate Market. St Magnus is the guild church of the Worshipful Company of Fishmongers and the Worshipful Company of Plumbers, and the ward church of the Ward of Bridge and Bridge Without.

A bomb which fell on London Bridge in 1940 during the Blitz blew out all the windows and damaged the plasterwork and the roof of the north aisle. However, the church was designated a Grade I listed building on 4 January 1950 and repaired in 1951, being re-opened for worship in June of that year by the Bishop of London.

By the early 1960s traffic congestion had become a problem and Lower Thames Street was widened over the next decade to form part of a significant new east-west transport artery. The setting of the church was further affected by the construction of a new London Bridge between 1967 and 1973.

St Magnus’s prominent location and beauty has prompted many mentions in literature. In Oliver Twist, Charles Dickens notes how, as Nancy heads for her secret meeting with Mr Brownlow and Rose Maylie on London Bridge, "the tower of old Saint Saviour’s Church, and the spire of Saint Magnus, so long the giant-warders of the ancient bridge, were visible in the gloom". The church’s spiritual and architectural importance is celebrated in the poem The Waste Land by T. S. Eliot, who adds in a footnote that "the interior of St. Magnus Martyr is to my mind one of the finest among Wren’s interiors".

Just inside the west door is a spectacular model of Old London Bridge.