1547, on the reconstitution of the court, he became the fourth officer, and master of the woods of the court this side the Trent. He probably retained this office till the court was incorporated in the exchequer in 1553 (Warton, pp. 15–19). He had been a privy councillor before 21 March 1544, and was frequently employed by the privy council on important business (Acts of P. C. vii. 281, viii. 328, ix. 111, 142).
Pope was not a regular commissioner for the suppression of the monasteries, but he received the surrender of St. Albans from Richard Stevenache on 5 Dec. 1539, and had exceptional facilities for obtaining grants of the abbey lands disposed of by his office. Of the thirty manors, more or less, which he eventually possessed by grant or purchase, almost all had been monastic property. There were conveyed to Pope, on 11 Feb. 1537, for a valuable consideration, the site and demesnes of Wroxton Priory, the manor or grange of Holcombe (Dorchester Priory), and other abbey lands in Oxfordshire. The manors of Bermondsey (4 March 1545) and Deptford (30 May 1554); the house and manor of Tittenhanger (23 July 1547), formerly the country seat of the abbots of St. Albans; and a town house, formerly the nunnery of Clerkenwell, ultimately fell, with much other property, into his hands. He thus became one of the richest commoners of the time.
Under Edward VI his want of sympathy with the Reformation largely withdrew him from public life (but cf. Wriothesley, Chron. ii. 7, 27). On the accession of Mary he was sworn of the privy council on 4 Aug. 1553. He was sheriff of Essex and Hertfordshire in 1552 and 1557, and was associated with Bonner, Thirlby, and North in a commission for the suppression of heresy on 8 Feb. 1557 (Burnet, Ref. ii. ii, records, No. 32). Pope may perhaps at the beginning of the reign have been attached to the Princess Elizabeth's household (Warton, p. 80). On 8 July 1556 he was selected to reside as guardian in her house (cf. Burnet, l. c. No. 33), but that he long had charge of Elizabeth is improbable. He clearly possessed the confidence of both the sisters, and was sent by Mary on 26 April 1558 to broach to Elizabeth an offer of marriage from Eric of Sweden (Cotton MS. Vitellius C. xvi. f. 334, in Burnet, l.c. No. 37; Warton, pp. 99–103). The commonly accepted accounts of the festivities given in honour of Elizabeth, mainly ‘at the chardges of Sir Thomas Pope,’ during 1557 and 1558, rest on no trustworthy evidence. Warton says that he derived them from copies made for him by Francis Wise of Strype's alleged transcripts of the then unpublished ‘Machyn's Diary’ in the Cottonian Library. An examination of Machyn's manuscript, after all allowance is made for the injury it sustained in the fire of 1731, proves that these passages were not derived from the source alleged, and it is probable that they were fabricated by Warton himself (cf. Warton, pref. pp. x–xiii, and pp. 86–91; Wiesener, La Jeunesse d'Elisabeth d'Angleterre, 1878, Engl. transl. 1879, vol. ii. chap. xi. and xii.; an account of the forgeries in English Historical Review for April 1896).
Meanwhile, like Lord Rich, Sir William Petre, Audley, and others, Pope was prompted to devote some part of his vast wealth to a semi-religious purpose. On 20 Feb. 1554–5 he purchased from Dr. George Owen (d. 1558) [q. v.] and William Martyn, the grantees, the site and buildings at Oxford of Durham College, the Oxford house of the abbey of Durham. A royal charter, dated 8 March, empowered him to establish and endow a college ‘of the Holy and Undivided Trinity’ within the university, to consist of a president, twelve fellows, and eight scholars, and a ‘Jesus scolehouse,’ at Hooknorton, for which four additional scholarships were subsequently substituted. On 28 March he executed a deed of erection, conveying the site to Thomas Slythurst and eight fellows and four scholars, who took formal possession the same day (Warton, App. ix.–xii.). The original members of the foundation were nearly all drawn from other colleges, chiefly Exeter and Queen's.
During 1555–6 he was engaged in perfecting the details of his scheme, repairing the buildings, and supplying necessaries for the chapel, hall, and library (ib. App. xvi.–xviii.). The members were admitted on the eve of Trinity Sunday, 30 May 1556, by Robert Morwent [q. v.], president of Corpus. The estates selected for the endowment were handed over as from Lady-day 1556, and comprised lands at Wroxton and Holcombe, with about the same amount in tithe, mostly in Essex, part of which he specially purchased from Lord Rich and Sir Edward Waldegrave. The statutes, dated 1 May 1556, which resemble other codes of the period, were drawn up by Pope and Slythurst with the assistance of Arthur Yeldard. Slight alterations were made by an ‘additamentum’ of 10 Sept. 1557. The rectory of Garsington, granted by the crown on 22 June 1557, was added to the endowment of the presidency on 1 Dec. 1557 (see Statutes of Trin. Coll. Oxf., printed by the University Commissioners, 1855). Warton's quotations from a letter alleging interest on the part of Elizabeth (p. 92) and Pole (p. 236) are probably fabrications.