In 1417 a dispute arose concerning who should take the place of honour amongst the Rectors in the City churches at the Whit Monday procession, a place that had been claimed from time to time by the Rectors of St Peter Cornhill, St Magnus the Martyr and St Nicholas Cole Abbey. The Mayor and Aldermen decided that the Rector of St Peter Cornhill should take precedence.
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. In pictures from the mid-16th century the old church looks very similar to the present-day St Giles without Cripplegate in the Barbican. According to the martyrologist John Foxe, a woman was imprisoned in the 'cage' on London Bridge in April 1555 and told to "cool herself there" for refusing to pray at St Magnus for the recently-deceased Pope Julius III.
Simon Lowe, a Member of Parliament and Master of the Merchant Taylors' Company during the reign of Queen Mary and one of the jurors who acquitted Sir Nicholas Throckmorton in 1554, was a parishioner. He was a mourner at the funeral of Maurice Griffith, Bishop of Rochester from 1554 to 1558 and Rector of St Magnus from 1537 to 1558, who was interred in the church on 30 November 1558 with much solemnity. In accordance with the Catholic church's desire to restore ecclesiastical pageantry in England, the funeral was a splendid affair, ending in a magnificent dinner.
Lowe was included in a return of recusants in the Diocese of Rochester in 1577, but was buried at St Magnus on 6 February 1578. Stow refers to his monument in the church. His eldest son, Timothy (died 1617), was knighted in 1603. His second son, Alderman Sir Thomas Lowe (1550–1623), was Master of the Haberdashers' Company on several occasions, Sheriff of London in 1595/96, Lord Mayor in 1604/05 and a Member of Parliament for London. His youngest son, Blessed John Lowe (1553–1586), having originally been a Protestant minister, converted to Roman Catholicism, studied for the priesthood at Douay and Rome and returned to London as a missionary priest. His absence had already been noted; a list of 1581 of "such persons of the Diocese of London as have any children ... beyond the seas" records "John Low son to Margaret Low of the Bridge, absent without licence four years". Having gained 500 converts to Catholicism between 1583 and 1586, he was arrested whilst walking with his mother near London Bridge, committed to The Clink and executed at Tyburn on 8 October 1586. He was beatified in 1987 as one of the eighty-five martyrs of England and Wales.
Sir William Garrard, Master of the Haberdashers' Company, Alderman, Sheriff of London in 1553/53, Lord Mayor in 1555/56 and a Member of Parliament was born in the parish and buried at St Magnus in 1571. Sir William Romney, merchant, philanthropist, Master of the Haberdashers' Company, Alderman for Bridge Within and Sheriff of London in 1603/04 was married at St Magnus in 1582. Ben Jonson is believed to have been married at St Magnus in 1594.
The patronage of St Magnus, having previously been in the Abbots and Convents of Westminster and Bermondsey (who presented alternatively), fell to the Crown on the suppression of the monasteries. In 1553, Queen Mary, by letters patent, granted it to the Bishop of London and his successors.
The church had a series of distinguished Rectors in the second half of the 16th and first half of the 17th century, including Myles Coverdale (Rector 1564-66), John Young (Rector 1566-92), Theophilus Aylmer (Rector 1592-1625), (Archdeacon of London and son of John Aylmer), and Cornelius Burges (Rector 1626-41). Coverdale was buried in the chancel of St Bartholomew-by-the-Exchange, but when that church was pulled down in 1840 his remains were removed to St Magnus.
On 5 November 1562 the churchwardens were ordered to break, or cause to be broken, in two parts all the altar stones in the church. Coverdale, an anti-vestiarian, was Rector at the peak of the vestments controversy. In March 1566 Archbishop Parker caused great consternation among many clergy by his edicts prescribing what was to be worn and by his summoning the London clergy to Lambeth to require their compliance. Coverdale excused himself from attending. Stow records that a non-conforming Scot who normally preached at St Magnus twice a day precipitated a fight on Palm Sunday 1566 at Little All Hallows in Thames Street with his preaching against vestments. Coverdale's resignation from St Magnus in summer 1566 may have been associated with these events. Separatist congregations started to emerge after 1566 and the first such, who called themselves 'Puritans' or 'Unspottyd Lambs of the Lord', was discovered close to St Magnus at Plumbers' Hall in Thames Street on 19 June 1567.