A lectureship at St Michael Crooked Lane, which was transferred to St Magnus in 1831, was endowed by the wills of Thomas and Susannah Townsend in 1789 and 1812 respectively. The Revd Henry Robert Huckin, Headmaster of Repton School from 1874 to 1882, was appointed Townsend Lecturer at St Magnus in 1871.
St Magnus narrowly escaped damage from a major fire in Lower Thames Street in October 1849.
During the second half of the 19th century the rectors were Alexander McCaul, DD (1799–1863, Rector 1850-63), who coined the term 'Judaeo Christian' in a letter dated 17 October 1821, and his son Alexander Israel McCaul (1835–1899, curate 1859-63, rector 1863-99). The Revd Alexander McCaul Sr was a Christian missionary to the Polish Jews, who (having declined an offer to become the first Anglican Bishop in Jerusalem) was appointed professor of Hebrew and rabbinical literature at King's College, London in 1841. His daughter, Elizabeth Finn (1825–1921), a noted linguist, founded the Distressed Gentlefolk Aid Association (now known as Elizabeth Finn Care).
In 1890 it was reported that the Bishop of London was to hold an inquiry as to the desirability of uniting the benefices of St George Botolph Lane and St Magnus. The expectation was a fusion of the two livings, the demolition of St George’s and the pensioning of "William Gladstone’s favourite Canon", Malcolm MacColl. Although services ceased there, St George’s was not demolished until 1904. The parish was then merged with St Mary at Hill rather than St Magnus.
The patronage of the living was acquired in the late 19th century by Sir Henry Peek Bt. DL MP, Senior Partner of Peek Brothers & Co of 20 Eastcheap, the country's largest firm of wholesale tea brokers and dealers, and Chairman of the Commercial Union Assurance Co. Peek was a generous philanthropist who was instrumental in saving both Wimbledon Common and Burnham Beeches from development. His grandson, Sir Wilfred Peek Bt. DSO JP, presented a cousin, Richard Peek, as rector in 1904. Peek, an ardent Freemason, held the office of Grand Chaplain of England. The Times recorded that his memorial service in July 1920 "was of a semi-Masonic character, Mr Peek having been a prominent Freemason". In June 1895 Peek had saved the life of a young French girl who jumped overboard from a ferry midway between Dinard and St Malo in Brittany and was awarded the bronze medal of the Royal Humane Society and the Gold Medal 1st Class of the Sociâetâe Nationale de Sauvetage de France.
In November 1898 a memorial service was held at St Magnus for Sir Stuart Knill Bt. (1824–1898), head of the firm of John Knill and Co, wharfingers, and formerly Lord Mayor and Master of the Plumbers' Company.
This was the first such service for a Roman Catholic taken in an Anglican church. Sir Stuart's son, Sir John Knill Bt. (1856-1934), also served as Alderman for the Ward of Bridge Within, Lord Mayor and Master of the Plumbers' Company. Until 1922 the annual Fish Harvest Festival was celebrated at St Magnus. The service moved in 1923 to St Dunstan in the East and then to St Mary at Hill, but St Magnus retained close links with the local fish merchants until the closure of old Billingsgate Market. St Magnus, in the 1950s, was "buried in the stink of Billingsgate fish-market, against which incense was a welcome antidote".
A report in 1920 proposed the demolition of nineteen City churches, including St Magnus. A general outcry from members of the public and parishioners alike prevented the execution of this plan. The members of the City Livery Club passed a resolution that they regarded “with horror and indignation the proposed demolition of 19 City churches” and pledged the Club to do everything in its power to prevent such a catastrophe. T. S. Eliot wrote that the threatened churches gave "to the business quarter of London a beauty which its hideous banks and commercial houses have not quite defaced. ... the least precious redeems some vulgar street ... The loss of these towers, to meet the eye down a grimy lane, and of these empty naves, to receive the solitary visitor at noon from the dust and tumult of Lombard Street, will be irreparable and unforgotten." The London County Council published a report concluding that St Magnus was "one of the most beautiful of all Wren's works" and "certainly one of the churches which should not be demolished without specially good reasons and after very full consideration." Due to the uncertainty about the church's future, the patron decided to defer action to fill the vacancy in the benefice and a curate-in-charge temporarily took responsibility for the parish. However, on 23 April 1921 it was announced that the Revd Henry Joy Fynes-Clinton would be the new Rector. The Times concluded that the appointment, with the Bishop’s approval, meant that the proposed demolition would not be carried out. Fr Fynes-Clinton was inducted on 31 May 1921.
The rectory, built by Robert Smirke in 1833-5, was at 39 King William Street. A decision was taken in 1909 to sell the property, the intention being to purchase a new rectory in the suburbs, but the sale fell through and at the time of the 1910 Land Tax Valuations the building was being let out to a number of tenants. The rectory was sold by the diocese on 30 May 1921 for £8,000 to Ridgways Limited, which owned the adjoining premises. The Vestry House adjoining the south west of the church, replacing the one built in the 1760s, may also have been by Smirke. Part of the burial ground of St Michael Crooked Lane, located between Fish Street Hill and King William Street, survived as an open space until 1987 when it was compulsorily purchased to facilitate the extension of the Docklands Light Railway into the City. The bodies were reburied at Brookwood Cemetery.