View of Eton College from the North, c.1640-60 Eton Collections | FDA-P.411-2010 (etoncollege.com)
The conflict most commonly known as the English Civil War(s) lasted from 1642 until 1651, and saw the execution of King Charles I in 1649. It was a conflict fuelled by political and religious differences and led to fundamental questioning of the respective roles of crown and parliament.
The turbulence within the country was reflected in English institutions, including that of Eton College. Both Royalists and Parliamentarians took an interest in the College, and it seems strange to the modern reader that a school should attract the attentions of parties involved in military conflict. In fact, even prior to the war, in 1635, a regiment of soldiers was billeted in the College, prompting a complaint to the Duke of Buckingham regarding the impact of this intrusion on ‘the youth repairing to the Schole, and lodging in the towne, with whom such companie do not well comport.”
During the conflict itself, the proximity of Windsor Castle which became a Parliamentary stronghold in 1642, meant that Eton became involved more directly in the military events. It seems, then, that the influence of the College, and its situation across the river from Windsor Castle, made it of potential interest. Once the civil war began, the college was even involved directly in the fighting when, in November 1642, Prince Rupert of the Rhine (Charles I’s nephew) made an unsuccessful attack on the castle. He is said to have set up his artillery, comprising four or five guns) on College land, to bombard the castle across the Thames: 
‘The bombardment lasted for about seven hours, leaving the town of Windsor mightily battered and ruined, and the inhabitants very much damnified.’ Thomason E127, Thomason Tracts
From a political perspective, the intellectual calibre of the Fellows and their potential influence explains the interest that both parties took in the College. John Hales, for example, described by the contemporary Royalist historian Clarendon as ‘one of the least men in the kingdom and one of the greatest scholars in Europe,’ attracted regular visits from Windsor courtiers. Ultimately, his scholarly credentials were insufficient to protect him and his refusal to subscribe to the pledge of loyalty to the ‘Commonwealth of England as it is now established, without a King or House of Lords’) cost him his Eton Fellowship.
At the outbreak of war, the Eton Register records that the Provost, Richard Steward, took the College seal and joined the king’s party in Oxford. At the same time many scholars, who were sons of Royalists, left the school to take up arms in the King’s cause. Inevitably, given the increasing dominance and confidence of Parliament, Steward was deprived of his post, on the basis of his ‘abandonment’ of the College and his affiliation to ‘those that have levied war against the Parliament.’
In due course, a new Provost was appointed, this time a man of impeccable Parliamentarian and anti-episcopal sympathies, Francis Rous who became the Speaker of the House of Commons in the ‘Barebones’ Parliament of 1653.
Rous appears to have been assiduous in his efforts to protect the material assets of the College, to the extent that he introduced motions in the House exempting Eton College from taxation, and permitting the election of Scholars to continue.
The Commons replaced incumbent Fellows with Puritans and, in 1649, all were required to subscribe to the pledge of loyalty described above. The headmaster, Nicholas Gray, also lost his post because of his Royalist sympathies. The Puritans at Eton were not unopposed, however: one of the Fellows, Thomas Weaver, convened meetings of members of disbanded choirs in his rooms, to perform the now proscribed sacred music. It seems that he was not unduly discreet about this as Colonel Venn, the Parliamentarian Governor of Windsor Castle, demanded why he was not satisfied with singing Psalms, in the approved Puritan fashion. Weaver is alleged to have retorted that ‘God was as well pleased with being served in tune as out of tune.’
Speaker Rous died in 1658/9, a few months after Oliver Cromwell, and was buried in Lupton’s Chapel, at his own request. Fellow John Oxenbridge, who preached the funeral sermon, took the opportunity to criticise Rous’s management of the College and his ‘schismatical tendencies.’ The latter point was somewhat ironic since Oxenbridge was, himself, no model of Anglican orthodoxy and was ejected from Eton in 1660.
As suggested above, the Restoration of 1660 brought a reckoning in its wake, not only for the Regicides and their supporters, but also for the Puritan incumbents at Eton. The Provost, Nicholas Lockyer, resigned from his post, as did the majority of the Puritan Fellows. The new king, Charles II, personally appointed Nicholas Monk as the new Provost, again underlining the importance of the College as a body of influential intellectuals.
Nicholas Monk and the Fellows set about erasing the outward signs of the Puritan ancien regime. Rous’s banners were removed from the chapel, and the memorial, composed by the poet Andrew Marvell to Jane Oxenridge, wife of the quondam Fellow John Oxenridge, was defaced.
Eton College was a microcosm of the this turbulent period, and its return to conforming Anglicanism similarly reflected the restoration of the episcopacy that accompanied the return of the monarchy.
By Marie Harrison, Museum Custodian
 Domestic State Papers. Charles 1. Vol. cclxxiv, No. 12 – cited in H.C. Maxwell-Lyte A History of Eton College, 1440-1875, p.228
 There had been rioting in the forests of Windsor, with some miscreants being sent to Newgate for stealing deer. The town adopted the Parliamentarian cause early, and raised funds in its support. R.R. Tighe and J.E. Davis Annals of Windsor, p.168
 John Vicars Magnalia dei Anglicana or England”s Parliamentary Chronicle
 Thomason E127 (10) Exceeding Joyfull Newes Out of Surrey. Shewing the proceedings of Prince Robert, as also of his attempt upon Windsor Castle.
 Lord Clarendon’s Life, Vol.1, p.62
 Eton Register vol. iii f,51 (cited in Maxwell-Lyte, p.238)
 Maxwell-Lyte p.169
 Ibid p.243
 Commons Journals Vol. iii p.456
 Tighe and Davis Annals of Windsor, Vol. ii, p.169
 Maxwell-Lyte p.254
 Wood Athenae Oxoniensis, Vol.iii. p.468