Originally, under the central body of the church was a rectangular, barrel vaulted crypt. This had chambers coming off its northern and southern sides formed by four brick ribs between the crypt and the external walls of the church. Before 1939, a chapel was located in it. During the Second World War, the crypt and a disused underground railway siding, accessible by an entrance on the north side of the churchyard were used as air raid shelters. This included bunk beds for people to sleep on. In 1949, a blast wall in the crypt used during the war was demolished. In 1973-74, the crypt was renovated and was used for social functions and also by a local scout group and in 1979, a small museum was located in the crypt. In 1993, due to persistent failures in the lighting, new lighting was installed. Social gatherings happened in the crypt and it even had its own bar. The crypt was completely redesigned during the 2005-07 restoration, with a new two room space being built under the whole floor plan of the church, including toilets and kitchen facilities. The crypt floor was also lowered by one metre and evidence for earlier burials were found.
After the 1734-36 rebuilding of the church, coffins were inserted in the north and south of the crypt. It is not clear if these burials were previous burials from the medieval and 17th century building. During the early 19th century, after 1823 based on evidence from coffin plates, a number of burials were re-interred in ossuary pits dug under the floors of the main crypt and its western rooms. In 1899, the crypt was cleared of 1,484 coffins which were re-interred in Brookwood Cemetery, Surrey. A further forty seven cases of human remains were removed from the church and interred at Brookwood Cemetery in June 1940, with the cost of this being £170 12s.
In 1997 an archaeological dig revealed human burials in lead coffins beneath the crypt floor, as well as evidence for the earlier church and also Roman occupation. Evidence was also found of a 17th century burial vault predating the existing church that was cut into the deposits made by the backfill of ‘Guy’s channel’; the Palaeolithic stream. This vault would have been beneath the location of the altar in the 17th century church.