The interior of the church was restored by Martin Travers in 1924, in a neo-baroque style, reflecting the Anglo-Catholic character of the congregation following the appointment of Henry Joy Fynes-Clinton as Rector. Fr Fynes, as he was often known, served as Rector of St Magnus from 31 May 1921 until his death on 4 December 1959 and substantially beautified the interior of the church.
Fynes-Clinton held very strong Anglo-Catholic views, and proceeded to make St Magnus as much like a baroque Roman Catholic church as possible. However, "he was such a loveable character with an old-world courtesy which was irresistible, that it was difficult for anyone to be unpleasant to him, however much they might disapprove of his views". He generally said the Roman Mass in Latin; and in personality was "grave, grand, well-connected and holy, with a laconic sense of humour". To a Protestant who had come to see Coverdale's monument he is reported to have said "We have just had a service in the language out of which he translated the Bible". The use of Latin in services was not, however, without grammatical danger. A response from his parishioners of "Ora pro nobis" after "Omnes sancti Angeli et Archangeli" in the Litany of the Saints would elicit a pause and the correction "No, Orate pro nobis."
Shrine of Our Lady of Walsingham in St Magnus the MartyrIn 1922 Fynes-Clinton refounded the Fraternity of Our Lady de Salve Regina. The Fraternity's badge is shown in the stained glass window at the east end of the north wall of the church above the reredos of the Lady Chapel altar. He also erected a statue of Our Lady of Walsingham and arranged pilgrimages to the Norfolk shrine, where he was one of the founding Guardians. In 1928 the journal of the Catholic League reported that St Magnus had presented a votive candle to the Shrine at Walsingham "in token of our common Devotion and the mutual sympathy and prayers that are we hope a growing bond between the peaceful country shrine and the church in the heart of the hurrying City, from the Altar of which the Pilgrimages regularly start".
Fynes-Clinton was General Secretary of the Anglican and Eastern Orthodox Churches Union and its successor, the Anglican and Eastern Churches Association, from 1906 to 1920 and served as Secretary to the Archbishop of Canterbury's Eastern Churches Committee from 1920 to around 1924. A Solemn Requiem was celebrated at St Magnus in September 1921 for the late King Peter of the Serbs, Croats and Slovenes.
At the midday service on 1 March 1922, J.A. Kensit, leader of the Protestant Truth Society, got up and protested against the form of worship. The proposed changes to the church in 1924 led to a hearing in the Consistory Court of the Chancellor of the Diocese of London and an appeal to the Court of Arches. Judgement was given by the latter Court in October 1924. The advowson was purchased in 1931, without the knowledge of the Rector and Parochial Church Council, by the evangelical Sir Charles King-Harman. A number of such cases, including the purchase of the advowsons of Clapham and Hampstead Parish Churches by Sir Charles, led to the passage of the Benefices (Purchase of Rights of Patronage) Measure 1933. This allowed the parishioners of St Magnus to purchase the advowson from Sir Charles King-Harman for £1,300 in 1934 and transfer it to the Patronage Board.
St Magnus was one of the churches that held special services before the opening of the second Anglo-Catholic Congress in 1923. Fynes-Clinton was the first incumbent to hold lunchtime services for City workers. Pathé News filmed the Palm Sunday procession at St Magnus in 1935. In The Towers of Trebizond, the novel by Rose Macauley published in 1956, Fr Chantry-Pigg's church is described as being several feet higher than St Mary’s Bourne Street and some inches above even St Magnus the Martyr.
In July 1937 Fr Fynes-Clinton, with two members of his congregation, travelled to Kirkwall to be present at the 800th anniversary celebrations of St Magnus Cathedral, Kirkwall. During their stay they visited Egilsay and were shown the spot where St Magnus had been slain. Later Fr Fynes-Clinton was present at a service held at the roofless church of St Magnus on Egilsay, where he suggested to his host Mr Fryer, the minister of the Cathedral, that the congregations of Kirkwall and London should unite to erect a permanent stone memorial on the traditional site where Earl Magnus had been murdered. In 1938 a cairn was built of local stone on Egilsay. It stands 12 feet high and is 6 feet broad at its base. The memorial was dedicated on 7 September 1938 and a bronze inscription on the monument reads "erected by the Rector and Congregation of St Magnus the Martyr by London Bridge and the Minister and Congregation of St Magnus Cathedral, Kirkwall to commemorate the traditional spot where Earl Magnus was slain, AD circa 1116 and to commemorate the Octocentenary of St Magnus Cathedral 1937".