The Civil War 

Although the town of Oxford itself supported the Parliamentary cause in the English Civil War, the powerful University was staunchly Royalist and, as a result, the city served as a home base for King Charles during the period.

Specifically, the University housed King Charles at Christ Church College between 1642 and 1646, while Queen Henrietta Maria stayed at Merton.

Oliver Cromwell
Once the war was over though, Oxford suffered for its Royalist support when in 1650 Oliver Cromwell was made Chancellor of the University and many heads of colleges were replaced with Cromwell supporters. In 1651, Parliament ordered the city to be slighted - destroying its defences.