Robert Hovenden, a Canterbury man, was elected Warden in 1571 at the age of twenty-seven. He was the youngest Warden ever to be elected and was to serve longer than any other before or since, dying in office forty-three years later. During his long tenure he showed himself to be a notable disciplinarian and a man jealous of the College's property. He defended, tooth and nail, the College's interest, even against Queen Elizabeth when she claimed College land at nearby Stanton Harcourt and demanded a peppercorn lease of the College's woods at Edgware in Middlesex; he commissioned over 100 cadastral maps of the College's estates; and he set its archive in order. He was also (and less admirably) successful in furthering the interests of his own kin in the bestowal of fellowships and beneficial leases, and in introducing a large number of undergraduates as servientes into the college – an influx which did not survive the Commonwealth, though there were four Bible Clerks on the establishment until 1924. He acquired land to the east and north of the range, added in 1550-3, and built on part of it the twin-gabled study (shown in David Loggan's view of 1675) which was pulled down in 1703 when the new lodgings were built. But his most notable addition to the College fabric is the fine heraldic ceiling in the Old Library. This was inserted in 1598 when the original – and by then overflowing – lectern desks were replaced by standing presses on the Merton College model.

Hovenden's two successors were unremarkable, but under one of them, Richard Astley (Warden 1618-36), we have, in 1633, a reference to the College totem - the mallard - and to the ceremonies connected with it. These included a circumambulation of the College by the Fellows, which, according to the Visitor's letter, had led in the previous year to 'barbarously unbeseeming conduct' involving doors and gates. Rooftop mallard circumambulations are known to have taken place on All Souls Day or St Hilary's Day (14 January, the first day of Hilary Term) in 1701, 1801, and - in a more seemly fashion - in 1901 and 2001; the accompanying Mallard Song is still sung at College gaudies.

Astley's successor, Gilbert Sheldon, the future Archbishop of Canterbury, who was Warden from 1636 to 1648 and from 1660 to 1661, made his mark in office. Not surprisingly, with Archbishop Laud as college Visitor and Chancellor of the University, and with Sheldon as Warden, attention was given to the fabric and arrangement of the chapel. Later writers have, however, erred in suggesting that it was Sheldon rather than Astley who courageously but vainly opposed Laud's high-handed if well-judged 'nomination' of Jeremy Taylor to a fellowship in 1635.