The chapel was founded in 1157, taking eighty eight years to complete, as the chapel of the Benedictine Convent of St Mary and St Radegund. Jesus College was founded in 1496 and following dissolution of the convent the college took over the precincts. Two thirds of what had been the nave were replaced with College rooms. During the reformation the chapel was reordered several times, according to the prevailing taste and state religion, and the eighteenth century saw major restoration in order to add the fashionable Classical features.
Between 1846 and 1849 the Chapel was again restored, reversing earlier adaptions and introducing the fashionable Gothic revival taste. That most-fashionable of Victorian Gothic revival designers, Augustus Pugin, was appointed by the College. Replacing the 18th century plaster ceiling with a 13th century style high-pitched roof, and replacing the 18th century Perpendicular east window with three tall lancet windows that reflected a much earlier design. Norman windows were discovered in the north wall which were preserved as recessed arches, and Pugin installed stained glass windows to his own design in 1850. A full choral service on All Saints Day 1849 heralded the reopening of the Chapel, and Pyne visited in 1856 to record the newly-refurbished chapel in this watercolour. Later, in 1867, William Morris undertook a splendid redecoration of the ceiling.