By the time the Long Parliament met, the universities, like the cathedral churches, were closely associated in the minds of anti-Laudians with the religious policies and beliefs of the Caroline regime. They were seen as the headquarters of Arminian ideas and practices, and of the ‘new popery’ generally, and consequently their reformation was high on the parliamentary agenda – although ultimately a thorough-going purge was to be delayed by the pressure of other business and then, as far as Oxford was concerned, by the war. While a broad reformation of the universities was seen to be needed to prevent the spread of dangerous religious ideas (such as those that challenged Calvinist tenets), it was important, too, that the chapels and churches be physically cleansed.

Both Oxford and Cambridge had undertaken a good deal of building work and refurbishment in the early decades of the seventeenth century, including the ‘beautifying’ of college chapels. This was not simply a product of the new Laudian-Arminian ideas. While the phenomenon gained its greatest momentum in the 1630s, under Laud's chancellorship of Oxford, the trend towards a less austere approach to church decoration began earlier. At Wadham chapel the erection of the great east window Crucifixion and side windows depicting apostles and saints was started in 1613. Laud, as president of St John's College, introduced rich altar furnishings and a costly organ into the chapel and in 1619 installed a picture of St John the Baptist in the east window.