The Great Fire of London in September 1666 gutted the mediaeval City of London, destroying 13,200 houses, St Paul’s Cathedral and 87 parish churches. St Magnus stood less than 300 yards from the bakehouse of Thomas Farriner in Pudding Lane where the fire started and was, after St Margaret New Fish Street, the second church to be destroyed.
The Mischiefs by Fire Act 1708 and the Fires Prevention (Metropolis) Act 1774 placed a requirement on every parish to keep equipment to fight fires. The church owns two 18th century manual fire engines made for St Michael, Crooked Lane by John Bristow, of 12 Church Lane, Whitechapel, London (repainted in 1836 and inscribed with the names of the two churchwardens). One of these is on display in the narthex of the church. The other was lent to the London Fire Brigade Museum.
In January 1765 the church had a policy with Hand in Hand Insurance in the sum of £1,000, of which £300 related to the tower and £700 related to the body of the church including the pews and altar.