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 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.
Humphrey Gower was at this time Master of the College; he was of Puritan origin, and entered the College during the Commonwealth. After the Restoration he joined the Church of England, and though his sympathies were with the Nonjurors, he took the oaths and retained his mastership after the flight of King James. He had been for less than six months Master of Jesus before becoming Master of St. John's. Abraham de la Pryme, a member of St. John's, has handed down an irreverent jest on his appointment. "Our master, they say, is a mighty, high, proud man.... He came from Jesus College to be master here, and he was so sevear that he was commonly called the divel of Jesus; and when he was made master here some unlucky scholars broke this jest upon him--that now the divel was entered into the heard of swine; for us Johnians are abusively called hoggs."