The Presbyterian Chinese congregation worshipped at 110 Lt Bourke Street from about 1919 before moving in 1952 when the building was sold. After a temporary move to 123 Lt Bourke Street (Chinese Anglican church) they moved to share premises with the Chinese Methodists at 196 Lt Bourke Street.On 30 April 1944 the Chinese Mission became the Chinese Presbyterian Church with the ordination of George Wong Loy and David Poon as elders of the congregation of the Chinese Church.

In 1983 they were informed they had to move from 196 Lt Bourke Street and on Christmas Day 1983 they started the move to the Malvern Presbyterian Church at 163 Wattletree Road, Malvern at the invitation of Rev Wally Beecher. The move was complete by 1 Jan 1984. In 2000 the Presbytery of Melbourne East approved the amalgamation of the Malvern Presbyterian Church and the Malvern Chinese Presbyterian Church which took place on 10 Sep 2000.