The reign of Queen Mary did not extend over much more than five years, but while it lasted a resolute and unflinching effort was made to re-establish the Roman Catholic faith.
The accession of Queen Elizabeth resulted in an equally rapid and fundamental revolution of opinion on the most vital points which can interest mankind. A few selected extracts from the College Account Books for this period bring before us, with almost dramatic effect, the changes which occurred. (Queen Mary succeeded in 1553, Queen Elizabeth on 17th November 1558.)
"1555, To the joyner for setting up the rood, 2d.; A new graell printed in parchment 40s.;—1556, In Spanish money given to the goldsmyth by Mr Willan to make a pixe to the highe Aultar, 24s. 11d.; A redde purple velvet cope, with the border of imagrie, having the assumption of our Ladie behinde and three little angels about her and the greater being full of floure de luces, 46s. 8d.;—1557, To William Allom for two antiphoners, one masse book and hymnal and processioners, £6 13s. 4d."
"1558, To John Waller and his man for a dayes working pulling down the hye Altar and carrying it away 20d.; For pulling down the aulter in Mr Ashton's Chapel 6d.; 1563, Received for certain old Albes and other popishe Trashe, sold out of the Revystry the last yere, 26s. 10d.; Paid to Mr Baxter for ten Geneva psalters and six service psalters, bought at Christmas last, 22s."
This last entry gives us the key to the troubles at St. John's; the Marian exiles had returned with strong Calvinistic leanings. The unrest was, of course, not confined to St. John's, but was general throughout the University. But for the greater part of the reign of Elizabeth there was a strong leaning toward Puritanism in the College. There was a rapid succession of Masters, most of whom were thrust on the College by Court influence; and about this time the Fellows of St. John's acquired the reputation of being "cunning practitioners" in the art of getting rid of unpopular Masters.
Queen Elizabeth visited Cambridge in August 1564, and was received with all honour. She rode into the Hall of St. John's on her palfrey and listened to a speech from Mr. Humphrey Bohun, one of the Fellows, in which for the last time the restitution of the Lady Margaret's estates was hinted at, without result.
Richard Longworth, a man of Presbyterian sympathies, was at this time Master. In 1565 he, with the Fellows and scholars, appeared in Chapel without the surplice. Lord Burghley, as Chancellor of the University, wrote a sharply worded letter to Longworth, expressing his grief that such a thing should happen in "my dear College of St. John's"; adding, "truly no mishap in all my service did ever plunge me more grievously."
Fortunately affairs were in strong and capable hands. With the authority and in the name of Queen Elizabeth, Whitgift, at this time Master of Trinity, afterwards Archbishop of Canterbury, and Cecil provided new statutes for the University in 1570, and for St. John's in 1580. By these much more power was put in the hands of the Master, and government rendered easier to a resolute man.
Matters improved, if not at once, at least gradually, and the Anglican rule became firmly established. But during the mastership of William Whitaker (1586-1595) we still hear of troubles with "Papists." Whitaker was a learned scholar and an acute theologian, but he does not seem to have been a ruler of men or a judge of character. He got involved in an unfortunate dispute with Everard Digby, one of the Fellows, a man of considerable literary reputation, but of a turbulent disposition. Whitaker, who clearly wanted to get rid of Digby, seized upon the pretext that his bill for a month's commons, amounting to 8s. 7¼d., was left unpaid, and deprived Digby of his fellowship. An appeal was lodged with Whitgift and Cecil, who ordered Whitaker to reinstate Digby. Whitaker replied that Digby was a Papist, was wont to blow a horn in the Courts and to holloa after it, and that he had threatened to put the President in the stocks! He seems to have succeeded in getting rid of Digby for good.
On the death of Whitaker in 1595, Richard Clayton became Master. If not a brilliant scholar, he commanded respect, and the tenor of many letters which have come down from that time shows that the Fellows in residence were on good terms with each other, and with those of the Society who had gone out into the world. The College was prosperous, and the building of the Second Court was the visible sign of returned efficiency. Clayton lived on into the reign of King James I., dying 2nd May 1612; besides being Master of St. John's, he was also Dean of Peterborough and a Prebendary of Lincoln.