In 876 Exeter (then known as Escanceaster) was attacked and briefly captured by the Danes. Alfred the Great drove them out the next summer, and in the following years made Exeter one of the four burhs in Devon, repairing the Roman city walls in the process. In 893 the city held off another siege by the Danes.

In about 928 King Athelstan caused the walls to be thoroughly repaired and at the same time drove out the Britons from the city. It is not known whether or not these Britons had lived in the city continuously since Roman times they may have been immigrants from the countryside when Alfred made the city a burh. According to William of Malmesbury, they were sent beyond the River Tamar, thereby fixing that river as the boundary of Devonshire, though Athelstan may have been restoring an old Dumnonian boundary. The quarter vacated by the Britons was then apparently adapted as "the earl's burh", and was still named Irlesberi in the 12th century.

In 1001 the Danes again failed to get into the city, but they were able to plunder it in 1003 because they were let in, for unknown reasons, by the French reeve of Emma of Normandy, who had been given the city as part of her dowry on her marriage to Æthelred the Unready the previous year.[

In 1067, possibly because Gytha Thorkelsdóttir, mother of King Harold, was living in the city, Exeter rebelled against William the Conqueror who promptly marched west and laid siege. After 18 days William accepted the city's honourable surrender in which he swore an oath not to harm the city or increase its ancient tribute. However, William quickly arranged for the building of Rougemont Castle to ensure the city's compliance in future. Properties owned by Saxon landlords were transferred into Norman hands, and on the death of Bishop Leofric in 1072, the Norman Osbern FitzOsbern was appointed his successor.

In 1136, early in the Anarchy, Rougemont Castle was held against King Stephen by Baldwin de Redvers. Redvers submitted only after a three month siege, not when the three wells in the castle ran dry, but only once the large supplies of wine in the garrison that they were using for drinking, baking, cooking and for putting out the fires started by the besiegers, were exhausted.

The city held a weekly market for the benefit of its citizens from at least 1213, and by 1281 Exeter was the only town in the south west to have three market days per week. There are also records of seven annual fairs, the earliest of which dates from 1130, and all of which continued until at least the early 16th century.

In 1537, the city was made a county corporate. In 1549 the city successfully withstood a month-long siege by the Prayer Book rebels. The Livery Dole Almshouses and Chapel at Heavitree were founded in March 1591 and finished in 1594. They can still be seen today in the street which bears the name Livery Dole.

The city's motto, Semper fidelis, is traditionally held to have been suggested by Elizabeth I, in acknowledgement of the city's contribution of ships to help defeat the Spanish Armada in 1588; however its first documented use is in 1660.