In 1888, Bishop Edward Bickersteth established the St. Andrew's Brotherhood in buildings adjoining the church to provide living quarters for unmarried clergy and a structured educational environment for seminarians.

The St. Hilda's Mission for women, also established by Bickersteth in 1888, was located close by at Azabu Nagazakacho, expanding on work begun by Alice Hoar, the first woman missionary of the SPG to reach Japan in 1875.

[9][10] Sir Ernest Satow, the British Envoy to Japan during the late 1890s, was an active supporter of the Diocese of South Tokyo,[11] his published diaries record attending services, vestry meetings and social functions at the church.

St. Andrew's Church has received many prominent visitors over the years, notable on Good Friday, April 14, 1922, were the crowds lining the route for the visit of Edward, Prince of Wales as a part of his four-week official tour of Japan.

Isaac Hidetoshi Nosse, resisted government pressure and police harassment during the Second World War to enable the church to retain its land, buildings and distinctive Anglican identity.