In 1107 William Warelwast, a nephew of William the Conqueror, was appointed to the see, and this was the catalyst for the building of a new cathedral in the Norman style. Its official foundation was in 1133, during Warelwast's time, but it took many more years to complete. Following the appointment of Walter Bronescombe as bishop in 1258, the building was already recognised as outmoded, and it was rebuilt in the Decorated Gothic style, following the example of nearby Salisbury. However, much of the Norman building was kept, including the two massive square towers and part of the walls. It was constructed entirely of local stone, including Purbeck Marble. The new cathedral was complete by about 1400, apart from the addition of the chapter house and chantry chapels.

Like most English cathedrals, Exeter suffered during the Dissolution of the Monasteries, but not as much as it would have done had it been a monastic foundation. Further damage was done during the English Civil War, when the cloisters were destroyed. Following the restoration of Charles II, a new pipe organ was built in the cathedral by John Loosemore. Charles II's sister Henrietta Anne of England was baptised here in 1644. During the Victorian era, some refurbishment was carried out by George Gilbert Scott. As a boy, the composer Matthew Locke was trained in the choir of Exeter Cathedral, under Edward Gibbons, the brother of Orlando Gibbons. His name can be found scribed into the stone organ 'screen'.