A bomb which fell on London Bridge in 1940 during the Blitz of World War II 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, William Wand. The architect was Laurence King. Restoration and redecoration work has subsequently been carried out several times, including after a fire in the early hours of 4 November 1995. Cleaning of the exterior stonework was completed in 2010.
Some minor changes were made to the parish boundary in 1954, including the transfer to St Magnus of an area between Fish Street Hill and Pudding Lane. The site of St Leonard Eastcheap, a church that was not rebuilt after the Great Fire, is therefore now in the parish of St Magnus despite being united to St Edmund the King.
Fr Fynes-Clinton marked the 50th anniversary of his priesthood in May 1952 with High Mass at St Magnus and lunch at Fishmongers' Hall. On 20 September 1956 a solemn Mass was sung in St Magnus to commence the celebration of the 25th anniversary of the restoration of the Holy House at Walsingham in 1931. In the evening of that day a reception was held in the large chamber of Caxton Hall, when between three and four hundred guests assembled.
Fr Fynes-Clinton was succeeded as rector in 1960 by Fr Colin Gill, who remained as incumbent until his death in 1983. Fr Gill was also closely connected with Walsingham and served as a Guardian between 1953 and 1983, including nine years as Master of the College of Guardians. He celebrated the Mass at the first National Pilgrimage in 1959 and presided over the Jubilee celebrations to mark the 50th anniversary of the Shrine in 1981, having been present at the Holy House's opening. A number of the congregation of St Stephen's Lewisham moved to St Magnus around 1960, following temporary changes in the form of worship there.
In 1994 the Templeman Commission proposed a radical restructuring of the churches in the City Deanery. St Magnus was identified as one of the 12 churches that would remain as either a parish or an 'active' church. However, the proposals were dropped following a public outcry and the consecration of a new Bishop of London.
The parish priest since 2003 has been Fr Philip Warner, who was previously priest-in-charge of St Mary's Church, Belgrade (Diocese in Europe) and Apokrisiarios for the Archbishop of Canterbury to the Serbian Orthodox Church. Since January 2004 there has been an annual Blessing of the Thames, with the congregations of St Magnus and Southwark Cathedral meeting in the middle of London Bridge.
On Sunday 3 July 2011, in anticipation of the feast of the translation of St Thomas à Becket (7 July), a procession from St Magnus brought a relic of the saint to the middle of the bridge. David Pearson specially composed two new pieces, a communion anthem A Mhànais mo rùin (O Magnus of my love) and a hymn to St Magnus Nobilis, humilis, for performance at the church on the feast of St Magnus the Martyr, 16 April 2012.
In addition to liturgical music of a high standard, St Magnus is the venue for a wide range of musical events. The Clemens non Papa Consort, founded in 2005, performs in collaboration with the production team Concert Bites as the church's resident ensemble. The church is used by The Esterhazy Singers for rehearsals and some concerts. The band Mishaped Pearls performed at the church on 17 December 2011. St Magnus's organist, John Eady, won a composition competition for a new choral work for the Feast of Pentecost with a setting of Veni Sancte Spiritus, which was first performed at St Paul's Cathedral on 27 May 2012. St Magnus featured in the television programme Jools Holland: London Calling, first broadcast on BBC2 on 9 June 2012. The Platinum Consort made a promotional film at St Magnus for the release of their debut album In the Dark on 2 July 2012.