Between the late Saxon period and 1209 there was a series of wooden bridges across the Thames, but in that year a stone bridge was completed. The work was overseen by Peter de Colechurch, a priest and head of the Fraternity of the Brethren of London Bridge. The Church had from early times encouraged the building of bridges and this activity was so important it was perceived to be an act of piety - a commitment to God which should be supported by the giving of alms. London’s citizens made gifts of land and money "to God and the Bridge". The Bridge House Estates became part of the City's jurisdiction in 1282.
Until 1831 the 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 à 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. After some years of rivalry a dispute arose between the church and the chapel over the offerings given to the chapel by the pilgrims. The matter was resolved by the brethren of the chapel making an annual contribution to St Magnus. At the Reformation the chapel was turned into a house and later a warehouse, the latter being demolished in 1757-58.
The church grew in importance. On 21 November 1234 a grant of land was made to the parson of St Magnus for the enlargement of the church. The London eyre of 1244 recorded that in 1238 "A thief named William of Ewelme of the county of Buckingham fled to the church of St. Magnus the Martyr, London, and there acknowledged the theft and abjured the realm. He had no chattels." Another entry recorded that "The City answers saying that the church of ... St. Magnus the Martyr ... which [is] situated on the king's highway ... ought to belong to the king and be in his gift". The church presumably jutted into the road running to the bridge, as it did in later times. In 1276 it was recorded that "the church of St. Magnus the Martyr is worth £15 yearly and Master Geoffrey de la Wade now holds it by the grant of the prior of Bermundeseie and the abbot of Westminster to whom King Henry conferred the advowson by his charter."
In 1274 "came King Edward and his wife (Eleanor) from the Holy Land and were crowned at Westminster on the Sunday next after the Feast of the Assumption of Our Lady (15 August), being the Feast of Saint Magnus (19 August); and the Conduit in Chepe ran all the day with red wine and white wine to drink, for all such as wished." Stow records that "in the year 1293, for victory obtained by Edward I against the Scots, every citizen, according to their several trade, made their several show, but especially the fishmongers" whose solemn procession including a knight "representing St Magnus, because it was upon St Magnus' day".
An important religious guild, the Confraternity de Salve Regina, was in existence by 1343, having been founded by the "better sort of the Parish of St Magnus" to sing the anthem 'Salve Regina' every evening. The Guild certificates of 1389 record that the Confraternity of Salve Regina and the guild of St Thomas the Martyr in the chapel on the bridge, whose members belonged to St Magnus parish, had determined to become one, to have the anthem of St Thomas after the Salve Regina and to devote their united resources to restoring and enlarging the church of St Magnus. An Act of Parliament of 1437 provided that all incorporated fraternities and companies should register their charters and have their ordinances approved by the civic authorities. Fear of enquiry into their privileges may have led established fraternities to seek a firm foundation for their rights. The letters patent of the fraternity of St Mary and St Thomas the Martyr of Salve Regina in St Magnus dated 26 May 1448 mention that the fraternity had petitioned for a charter on the grounds that the society was not duly founded.
In the mid-14th century the Pope was the Patron of the living and appointed five rectors to the benefice.
Henry Yevele, the master mason whose work included the rebuilding of Westminster Hall and the naves of Westminster Abbey and Canterbury Cathedral, was a parishioner and rebuilt the chapel on London Bridge between 1384 and 1397. He served as a warden of London Bridge and was buried at St Magnus on his death in 1400. His monument was extant in John Stow's time, but was probably destroyed by the fire of 1666.
Yevele, as the King’s Mason, was overseen by Geoffrey Chaucer in his capacity as the Clerk of the King's Works. In The General Prologue of Chaucer's The Canterbury Tales the five guildsmen "were clothed alle in o lyveree Of a solempne and a greet fraternitee" and may be thought of as belonging to the guild in the parish of St Magnus, or one like it. Chaucer's family home was near to the bridge in Thames Street.