The College received its first benefactions of land from Principal Griffith Lloyd (1572-86), whose small bequest of Cardiganshire property came to the College after his widow's death in 1615, and from Bishop Herbert Westfaling of Hereford (d. 1602), one of thirteen commissioners named in Queen Elizabeth's second (1589) charter, whose bequest of two Herefordshire farms came early in 1603. (One of these, Sydcombe, at Dorstone, near Hay-on-Wye, remained in the College's possession until 2009.) Many small endowments, bequests of land, subscriptions towards building, and contributions towards the College library followed from well-wishers during the reigns of James I and Charles I, sometimes as the result of specific fund-raising campaigns. Principal Francis Mansell (1630-49), an ambitious developer, pulled down Thelwall's library and built the eastern half of the residential Second Quadrangle, probably to attract the sons of South Welsh gentry families, who occupied at least one of the two new staircases in some comfort. Ejected as a royalist in 1649, Mansell was reinstated in 1660, but was too broken in spirit to remain as Principal for more than a few months. His successor (1661-73) was his former pupil (Sir) Leoline Jenkins from Llanblethian, Glamorgan, a busy lawyer who combined his principalship with practising in London in the Court of Arches and High Court of Admiralty.
After twelve years as Principal, Jenkins left the country as a diplomat, and was later created a Secretary of State. On his death in 1685 he bequeathed the College a large complex of estates, acquired on his behalf by lawyer friends from members of the distressed, over-mortgaged landowning classes of the Restoration period. These comprised groups of farms in Northamptonshire, Gloucestershire, the Vale of Glamorgan and the Taff Valley mining area, and ten acres of the London estate of the Earls of Arundel across the Thames from their town house in the Strand. With money left by Jenkins, the College purchased further farms in west Oxfordshire, and, on his instructions, filled all sixteen College fellowships and (mainly graduate) scholarships. (Originally allocated eight of each, the College had officially supported sixteen of each since the Statutes came into force in 1622, but had enjoyed too small an income to be able to keep all of them filled at once.) Two fellows were to be allotted Greek and Latin lectureships which Jenkins endowed to further the study of the classics. Jenkins also endowed 'missionary fellowships' to encourage young clergymen to minister in the Navy and overseas, and increased the regular fellows' stipends, by dividends from his estate and other payments, to a more realistic figure than the previous £20 a year.
Jenkins left the College his library, which included many fine classical texts and works on international law, and set up a trust fund for the support of his old school at Cowbridge. His portrait hangs behind High Table in the College hall; while nearby hangs a portrait of his patron King Charles II, in an elaborate baroque frame, bequeathed by him to the College. The full-length portrait of Queen Elizabeth I behind High Table, attributed to Hilliard or his school, was presented to the College in 1687 by a former fellow, James Jeffreys, a brother of the infamous protégé of Charles II, Judge George Jeffreys.
Secured for the future by Jenkins's benefaction, the College received another important bequest in 1713. This came from a former member of the College, Edmond Meyricke, and comprised lands in North Wales and Carmarthen, with funds for the support of Bala Grammar School and for scholarships and exhibitions at Jesus for students from North Wales. More recent benefactions have included gifts of money for new buildings, books and equipment; funds for graduate scholarships, undergraduate travel abroad, and prizes; and bequests for general College purposes, the most recent of which, for £2m, has endowed three tutorial fellowships.