Charles I upheld the belief of the divine right of kings at a time when people felt that kings should only rule by the will of Parliament; his unwillingness to compromise with the new Puritan movement meant that a 'war without an enemy' was inevitable. Oxford was selected as the Royalist capital.

Although most of its citizens were so anti-Royalist that the King had to disarm them, the University was loyal to the Monarch. When he and his army of 5,500 had to escape from the city, across Port Meadow, it surrendered to the parliamentary victory with great reluctance. Cromwell became Chancellor in April 1646.

Subsequently a 'Parliamentary Visitation' was sent to reform and regulate the University which was exhausted and disrupted by the years of war. An uneasy relationship existed between the Parliamentarians and the academics until 1660, when Charles II was restored to the throne.