With the advent of the Stuart kings the practice arose of sending mandatory letters to Colleges, directing the election of named persons to fellowships. In theory it may have been correct enough; the statutes as enacted by Queen Elizabeth reserved to herself and her successors the power of rescinding or altering them. To direct that the statutory provisions as to elections should be dispensed with in favour of an individual was thus within the sovereign's power, however inconvenient it might prove in practice. One of the special grievances at St. John's was that King James directed the College to elect a Scotchman, George Seaton, M.A., to a fellowship, though there was none then actually vacant. The College obeyed, informing his Majesty that they had made their statutes wink to fulfil his bidding, and maintained an extra Fellow for a time. The practice was, however, followed by others; and Gwyn seems to have been deluged with letters from persons in high places, begging for his favour at elections. At some Colleges the device of "pre-elections" seems to have been resorted to; a promising man being elected to the next fellowship which should be vacant. Thus, when the vacancy became known, the College could, with a clear conscience, say that it had been already filled up; there is, however, no trace of this practice at St. John's.

On Gwyn's death in 1633 there was a disputed election to the mastership, which Charles I. settled by nominating William Beale. Beale was originally a Trinity man, but had been for about a year Master of Jesus. He was a supporter of Laud; he embellished the Chapel, and introduced a more ornate ritual; under his influence St. John's seems to have been the only College at Cambridge which fully complied with Laud's instructions. Thus when the Puritans got the upper hand, Beale and his College were the subject of their displeasure.

In 1642 King Charles applied to the University for supplies. The contribution of St. John's was £150 in money and 2065 ounces "grocers weight" of silver plate. The list of the pieces of plate and of the donors' names is but melancholy reading; suffice it to say that among those sent were pieces bearing the names of Thomas Wentworth, Lord Strafford, and of Thomas Fairfax. The fact that this plate actually reached the King did not endear the College to the parliamentary party. Oliver Cromwell surrounded the College, took Dr. Beale a prisoner, and, to equalise matters, confiscated the communion plate and other valuables.

Beale, after some imprisonment and wandering, escaped from England and became chaplain to Lord Cottington and Sir Edward Hyde (afterwards Lord Clarendon) in their embassy to Spain; he died at Madrid, and was there secretly buried. A number of the Fellows were also ejected, and for some time the College was used as a prison. The Chapel was stripped of the obnoxious ornaments, and other damage done. A little bundle of papers labelled "Receipts for Army taxes during the Commonwealth" still reposes, as a memento of these days, in the Muniment Room.

St. John's, which dabbled in Presbyterian doctrines during the days of Elizabeth, now had these imposed upon it by superior authority. The two Commonwealth Masters, John Arrowsmith (1644-1653) and Anthony Tuckney (1653-1661), were able men of Puritan austerity, the rule of the latter being the more strict; judging from the after careers of its members, the College was certainly capably directed. A well-authenticated College tradition relates that when, at an election, the President called upon the Master to have regard to the "godly," Tuckney replied that no one showed greater regard for the truly godly than himself, but that he was determined to choose none but scholars; adding, with practical wisdom, "They may deceive me in their godliness; they cannot in their scholarship."

On the Restoration, Dr. Peter Gunning, afterwards Bishop of Ely, was made Master; and the Earl of Manchester, who, as an officer of the Parliament, was the means of ejecting many of the Fellows, now directed that some of them should be restored to their places. An interesting College custom dates from this period: on the 29th of May in each year the College butler decorates the Hall and Kitchen with fresh oak boughs; there is no order to that effect, but—"it has always been done."

The College Arms

The rest of this century of the College existence, with the exception of one exciting event, passed quietly enough. Such troubles as there were in College were but eddies of the storms in the world outside. Of the "seven Bishops" sent to the Tower by King James II. in 1688, three were of St. John's: Francis Turner, Bishop of Ely (who had been Master of the College from 1670 to 1679); John Lake, Bishop of Chichester; and Thomas White, Bishop of Peterborough.

The event of College interest was the fate of the nonjuring Fellows. The Nonjurors were those who, on various grounds, honourable enough, declined to take the oath of allegiance to King William and Queen Mary. Under the law they were liable to be deprived of their places and emoluments. At St. John's twenty Fellows and eight scholars took up the nonjuring position. In the rest of the University there were but fourteen in all, and the same number at the University of Oxford. No explanation seems to be forthcoming as to why there was this preponderance of opinion at St. John's. It is difficult to believe that it was enthusiasm for the cause of James II.; for when in 1687 that King directed the University to admit Father Alban Francis, a Benedictine monk, to the degree of M.A. without making the subscription or taking the oaths required for a degree, Thomas Smoult and John Billers, members of the College (the latter afterwards a Nonjuror), maintained the right of the University to refuse the degree before the notorious Judge Jeffreys, after the Vice-Chancellor and Isaac Newton had been silenced.