His commissions include a line of windows in the north wall of the nave of Westminster Abbey; At St Peter's Parish Church, Huddersfield baldachino/ciborium, high altar and east window in memory of the dead of the Great War; St Mary's, Wellingborough; St Michael and All Angels, Inverness; the Lady Chapel at Downside Abbey, Somerset; the ciborium and House Chapel extension for the Society of St. John the Evangelist in Oxford (now St Stephen's House, Oxford) and St Cyprian's, Clarence Gate, London. Comper is noted for re-introducing the 'English altar', an altar surrounded by riddel posts. Comper designed a number of remarkable altar screens (reredos), inspired by medieval originals. Wymondham Abbey, Norfolk, has one of the finest examples.
Comper was knighted by King George VI in 1950. In 1960, he died in The Hostel of God (now Trinity Hospice) in Clapham. His ashes are buried beneath the windows he designed in Westminster Abbey.