During the Second World War, 32 members of St Mary Magdalene's died, and a memorial pulpit was put up in their memory. This was part of a massive renovation programme following the war, which involved the rebuilding of the Church organ. However, other major changes suddenly faced the Vestry. The Catholic Apostolic Church in Dudhope Crescent Road had closed down in 1944, and their Trustees were anxious to sell their large and beautiful church to another Christian organization. They were willing to sell the property for just £5,000, which even at that time was a stunning bargain. St Mary Magdalene's suddenly realized that they could achieve their long-held dream of moving to a larger church. The sacraments were moved from the aumbry in the old church to their new home on the evening of 12th February 1952. The Rectory was also sold and a new Rectory bought in Albany Terrace.
After these changes, Canon Drake moved to Edinburgh. His place was taken by Dean Matthew Gibson, who had been a curate at the old church during the war. The congregation had now acquired a very large building; but just at this moment, the Corporation of Dundee began to decant thousands of people to the new housing schemes on the outskirts of the city. The people were completely uprooted. They could no longer walk round the corner to the Church. They had to catch a bus. Over a period of eighteen years, the congregation shrank from 2,750 members to 839. The Dean worked long hours visiting, trying to keep in touch with all his people; but the tide was flowing against him and his own health failed. He died in January 1971.
Although there was still a sizeable congregation, the question arose as to whether the Episcopal Church needed eight churches in the city — placed where they were on the city side of the Kingsway. The new Rector, Rev William McAusland (1971–1979) felt that St Mary Magdalene's should be closed. He put his proposal to the Vestry in March 1976. The Vestry and congregation were naturally horrified at the suggestion, and a public meeting was held at which the congregation voted 90–13 in favour of keeping the church open. Bishop Luscombe blocked any immediate decision and suggested that the congregation should spend two years trying to build up the congregation and put the church on a sounder footing. In fact, many important property repairs, requiring urgent action, were delayed.