The church has two small transepts aligning with the easternmost bay of the nave.

The North transept is the St Nicholas Chapel: Here, before the Reformation, the ceremonies to elect a ‘Boy Bishop’ were held on 6th December. The inventory, now held in the Bristish Museum, describes the elaborate mitres and pastoral staff used by the ‘bishop’ and his ‘deacons’. One of the special coins struck to commemorate a Mancroft boy’s ‘episcopate’ can be seen in the Castle Museum. The transept now houses the treasury displaying some of Mancroft’s remarkable collection of church silver (one of the finest of any parish church in the country) including the Gleane and Thistle cups, and other historic artefacts and artworks. Church plate is also on display here from the neighbouring church of St Stephen.

Roof of the South Transcept

The South transept, which formerly housed the 1911 Hele organ , has become a quiet chapel dedicated to the Blessed Virgin Mary. The book of sorrow and loss is kept here and the chapel is reserved at all times for private prayer. The meditative cross with raised arms is the work of York Sculptor, Charles Gurrey.

The St Anne Chapel (South aisle) was once the meeting place for mothers and daughters who belonged to the medieval Guild of St Anne (similar to the present day Mother’s Union). The Chapel’s East window is by H. Hendrie (1921) and is a memorial to the dead of the Great War.

The Jesus Chapel (North aisle) is the earliest part of the present church and contains the tomb of Francis Windham. The East window of the chapel features a fine stained glass window with the theme of mountains commemorating a former vicar, Archdeacon Pelham Burn, who met his death in 1901, mountaineering in the Alps. The modern altar frontal and dorsal are the work of Isabel Clover. Weekday services are held in this chapel.