The accession of Edward VI., and the visitation of the University, brought serious trouble upon the College. The President, Owen Oglethorpe, was apparently prepared to accept the earlier stages of the Reformation movement, but he was not prepared to go so far as the party in power required. Some members of the College were of the more advanced school of the Reformers; and much irreverence, with a good deal of wanton destruction, was committed by them, encouraged by letters from the Protector inciting the College to the “redress of religion.” Oglethorpe was removed from the office of President, into which Walter Haddon, a person not eligible according to the statutes, was intruded, in spite of a petition from the Fellows, and the work of reformation proceeded according to the desire of the Council. Haddon is said to have sold many of the effects of the chapel, valued at about £1000, for about a twentieth part of that sum, and to have “consumed on alterations” not only the sum so received, but a larger sum of the “public money” of the College. It was fortunate for the society that the scheme of the Council for the total suppression of the choir, and the alienation of a corresponding part of the College revenue, had been promulgated while Oglethorpe was still President. Under his guidance, with considerable difficulty, the College managed to preserve this part of its foundation unimpaired.

Immediately on the accession of Queen Mary, Walter Haddon received, as appears from the Vice-President’s register, leave of absence on urgent private affairs, and his example was soon followed by those of the Fellows who had been especially notable for their zeal in the “redress of religion.” Laurence Humphrey, one of this party, obtained leave for the express purpose of conveying himself in transmarinas partes; and this leave of absence was continued to him at a later time provided that he did not resort to those towns which were known to be the refuge of heretics. He took up his abode forthwith at Zürich. As he was absent from the College during the whole of Mary’s reign, he is perhaps not a sufficient witness of the events of that time. He asserts that the Roman party had great difficulty in re-establishing the old order of things in College, and that the younger members of the society suffered many things at their hands. Of all this, however, there is no evidence in the Vice-President’s register, where most of the offences and almost all the penalties recorded during this period are of an ordinary kind.[204] Oglethorpe was restored to his Presidency, and was succeeded on his elevation to the See of Carlisle, by Arthur Cole, a Canon of Windsor.[205] During the tenure of Cole, and of his successor Thomas Coveney (whom the College chose in preference to three persons recommended by the Queen), there appear to have been differences of opinion on religious matters within the College, and some difficulties in enforcing the due attendance of its members at the chapel services; but there is no sign of what might be called a tendency to persecution on the part of the authorities. The most recalcitrant members of the society seem to have been the Bachelor Demies and Probationer Fellows. Coveney remained President for some time after Queen Elizabeth’s coronation by Oglethorpe; and in the interval between that event and the consecration of Archbishop Parker there are some indications in the register of religious strife within the College. The end of Coveney’s term of office was marked by a contest between himself and some of the Fellows, concerning matters of College business, in which he seems to have exceeded his power as President. He was deprived by Bishop Horn at a Visitation in 1561, on the ground, it is said, that he was a layman; but it might be at least doubtful whether the founder’s statutes strictly required the President to be in Holy Orders; and it is probable that the real reason for his deprivation lay in the fact that Horn regarded him as being too much “addicted to the Popish superstition.”

This fault at all events could not be laid to the charge of Laurence Humphrey, who succeeded him. Horn himself had reported that the members of the College, whom he expected to find of the same school as their President, were willing to accept the tests he proposed to them—to acknowledge the Queen’s supremacy, and to accept the Book of Common Prayer, and the Advertisements. Before Humphrey had been long President the College had ceased to be “conformable,” but its non-conformity was of the Puritan, not of the Romanizing, type. Humphrey himself had a strong objection to wearing a surplice, or using his proper academical dress, and many of his Fellows followed his example in this matter. It required more than one Visitation to induce compliance on such matters. Abuses of another kind, however, were left uncorrected, and even encouraged, by the Visitors. Many Fellowships were filled up by nominations from the Queen, or from the Bishop of Winchester, and it may be added that the persons nominated were not always model members of a College. There were many contentions between the Fellows, and between the President and the Fellows. The general impression given by reading the register of the time of Humphrey and his immediate successors is, that the College was becoming a home of disorder rather than of learning. Nicolas Bond, Humphrey’s successor, seems, however, in 1589 to have made some rather ineffectual efforts to provide for more regular and systematic study among its members. During his tenure of office the society received a visit from King James I., accompanied by his son Henry, then Prince of Wales, who was matriculated as a member of the College. The King was much impressed by the buildings, and greatly enjoyed his visit. The grotesque figures or “hieroglyphics” in the Cloister Quadrangle were painted, as it would seem, in honour of his coming, Moses in particular being adorned toga coerulea.

The College, which was Puritan under Humphrey, was even more Puritan under Bond, Harding, and Langton; with Langton’s successor, however, in 1626, the tide set in the contrary direction. Accepted Frewen, if, as his name suggests, he was of Puritan descent, was himself a supporter of Laud’s ecclesiastical policy, and acted with vigour both as President in his own College and as Vice-Chancellor in the University, for the restoration of discipline and good order. The numbers of the College had been increased during his predecessor’s time by the influx of a number of so-called “poor scholars,” whose connection with the College was very slight, and who seem to have in many cases been entered as members of the society by the mere authority of the person to whom they had attached themselves. Frewen made regulations on this subject, and these seem to have been re-inforced a few years later by a letter from the Visitor. Other matters he also took in hand with good effect, especially the restoration of the chapel, on which he seems to have spent large sums of his own, in addition to the corporate expenditure of the College. The windows of the ante-chapel (except the great west window) were part of Frewen’s work, the only part which has been left by the later restoration of 1832.

The outbreak of the Great Rebellion found the College converted from a nest of Puritans into a nest of Royalists and High Churchmen. The King’s demand for loans of money and plate was met with some difficulty, but without hesitation, by a loan of £1000 in money and by the delivery of plate to the value of about £1000 more. When the Parliamentary forces entered Oxford in September 1642 they found at Magdalen “certain Cavaliers in scholars’ habits,” who had “feathers and buff-coats” in their chambers. Some of the scholars, being malignant persons, “scoffed” at the invaders and “at the honourable Houses of Parliament,” and were accordingly made prisoners. Other members of the College had left Oxford a few days before with Byron’s horse, to join the King: among them was John Nourse, Fellow and Doctor of Civil Law, who fell at Edgehill. After that action the King entered Oxford, and Prince Rupert took up his quarters at Magdalen. The King’s artillery was placed in Magdalen College Grove, which served as a drill-ground for the regiment of scholars and strangers which was raised in 1644; batteries were erected in the Walks, and gunners exercised in the College meadows. The timber in the Grove was probably felled for use in the defensive works.[206] A curious contrast to this military preparation was furnished by the imposing ceremonial of Frewen’s consecration as Bishop of Lichfield, which took place in the chapel of the College in April 1644.[207]

Some members of the College were as active on the side of the Parliament as those who remained in Oxford were on the side of the King. A Demy named Lidcott was deprived of his place for having been in arms against the King, serving in Essex’s army as an “antient” of a foot company. A far more celebrated member of the Parliamentary party, John Hampden, had formerly been a member of the College which was the head-quarters of the commander of the troops against whom he fought at Chalgrove.

After the surrender of Oxford, considerable havoc was wrought in the chapel of the College by the Parliamentary troops, who destroyed, among other things, the glass of many of the windows. The organ was appropriated by Cromwell to his own use, and removed by him to Hampton Court, whence it was brought again after the Restoration.[208] The Parliamentary Visitors of the University found few members of the College willing to submit to their authority. The President, Dr. John Oliver, and the greater part of the members were ejected, and the bursar, who obstinately refused to give up keys or papers, was imprisoned. The tenants of the College, however, persisted in paying their rents to him, and special injunctions had to be given to prevent them from doing so. The places in College rendered vacant by expulsions were filled up by the importation of Independents and Presbyterians, Dr. John Wilkinson, a former Fellow, being made President. He was succeeded two years later by Goodwin, a gloomy person, whose examination of a candidate for a Demyship has been recounted by Addison in the Spectator.[209] The records of the events in College during the Commonwealth are very scanty. One of the most remarkable proceedings of the intruders was the appropriation and division among themselves of a sum of money which they found in the muniment-room; this was the fund provided by the Founder for special necessities, which had remained untouched since 1585, and the existence of which had perhaps been forgotten. It was for the most part in ancient coinage, the pieces being of the kind known as “spur royals.” Of these a hundred fell to the share of Wilkinson, who seems to have been the instigator of the division; nine hundred more were divided among the thirty Fellows, and the Demies and others, including the servants, received portions of the spoil. Before the Restoration, however, some of the recipients restored the pieces they had obtained, and the greater part of the money was actually repaid in course of time. The fund, under more modern financial arrangements, no longer remains in the muniment-room, but some of the old coins are still preserved there.

On the Restoration the ejected members of the College, or those who were left, were restored to their home. They included the President, seventeen Fellows and eight Demies.[210] Dr. Oliver, however, did not long survive his return; and upon his death began a time of trouble. Charles II. recommended as his successor Dr. Thomas Pierce, a divine who had done much service in the defence of the Church against her assailants, but whom the Fellows, who perhaps knew him better than the King were unwilling, as it seems, to elect. Charles however enforced obedience by a letter as peremptory as any communication which the College afterwards received from his brother, and Dr. Pierce became President. The result was a long warfare between Pierce, the Fellows, and the Visitor, Bishop Morley, whose intentions seem to have been better than his judgment. At last the King interfered, and the difficulty was solved by the promotion of Dr. Pierce to the Deanery of Salisbury, where he found scope for his energies in a controversy with his Bishop. Dr. Henry Clerk was now recommended by the King, and elected by the Fellows, and the society was at peace for some years. That peace was again disturbed, on Dr. Clerk’s death, by the action of James II., who attempted to force upon the College as its President a man unqualified by statute and disqualified by notorious immorality. The history of the struggle which followed is too well known to need repetition here.[211] The Fellows almost unanimously chose one of their own number, and supported him, when duly elected, against the King’s second nominee. In the end, after a year’s exile, they were restored to their College, under Dr. John Hough, the President of their own choice, by the Bishop of Winchester, acting on instructions from the King.

The Revolution brought with it new causes of disquiet, and some members of the College were again ejected as Nonjurors. The great majority, however, of those who had contended against the usurpation of James were content to submit themselves to the new Sovereigns, and retained their places. The most notable member who was thus lost to the College was Dr. Thomas Smith, a man of much learning and ability, and a steady and uncompromising Royalist. In 1689 occurred what was afterwards known as the “Golden Election” of Demies, which included, besides others less known, Hugh Boulter, afterwards Archbishop of Armagh, Smallbrook, afterwards Bishop of St. David’s and later of Lichfield, the notorious Henry Sacheverell, and Joseph Addison, the most celebrated member of the College since the Revolution. The residence of Addison in College was not prolonged beyond his year of probation as Fellow; but he has left a memory of himself in the fact that his name has been attached to a portion of the Walks. These it would seem in his time did not extend beyond what is now called Addison’s Walk, but was formerly known as “Dover Pier.”

The members of the College who remained seem to have maintained friendly relations with those who had withdrawn from it as Nonjurors, and even at this time, and certainly after the accession of George I., the sympathy of many among the Fellows was with the exiled rather than with the reigning branch of the Royal House. During the first half of the eighteenth century, indeed, politics flourished in the society more than learning; and although Gibbon’s picture of the condition of the College during his brief residence is rather highly coloured, it cannot be doubted that the general decline of academic activity which affected many of the Colleges in Oxford during the last century, affected Magdalen in no slight degree. A large part of the attention of the society seems to have been given to plans for the rearrangement or the destruction of the College buildings, and for the re-construction of the College on the pattern adopted in what are known as the “New Buildings,” erected in 1735. Some amazing designs for “College improvements” remain in the library, as a memorial of the architectural ambitions of this period. Among the Presidents of the eighteenth century, if we except Dr. Routh, whose lengthened tenure extended over the last years of that century and the first half of the nineteenth, there is but one name of mark—that of George Horne, afterwards Bishop of Norwich, once widely-known by his Commentary on the Psalms. Nor are there many names of mark among the other members of the College in the same century. The learning of Dr. Routh does not seem to have been shared in any conspicuous degree by more than a small proportion of those who passed through the College in his long Presidentship—though towards the end of that period Magdalen numbered among its members several men of note in different ways—James Mozley and William Palmer among theologians, Ferrier among philosophers, Roundell Palmer, now Lord Selborne, among lawyers, Conington among scholars, Charles Reade among novelists, Goldwin Smith among essayists, Charles Daubeny among those who laboured to advance the study of natural science.