A noteworthy provision was one whereby the lecturer was required to deliver his discourse not only in Latin, but also in English,' for the capacity of those that be not learned '(Strype, Life, ed. 1821, i. 17). Parker was at this time in but poor health, in consequence of which a grace was passed in 1536 by the Cambridge senate allowing him to preach with his head covered. In 1535 he proceeded B.D., and on 1 March 1537 was appointed chaplain to the king; in the following year he proceeded D.D. Although his name does not appear as one of the compilers of the 'Institution of a Christian Man' (1537), he took a deep interest in the work, and his devotion to theological studies continued unabated. He did not, however, escape the imputation of heresy; and in 1539 he was formally accused before Lord-chancellor Audley by one George Colt and other inhabitants of Clare, the allegations against him being the use of language that was either unauthorised or disloyal on such subjects as the Roman observance of Easter, the veneration of relics, and the purposes to which taxes were converted by the crown. Audley dismissed all the charges as frivolous, and exhorted Parker 'to go on and fear not' (manuscript note on letter from Parker to Dr. Stokes, in Corp. Coll. Library). That he lost nothing in favour with those in power may be inferred from his presentation in 1542 to the living of Ashdon in Essex, and to a prebendal stall at Ely. On 30 April 1544 he resigned the rectory of Ashdon, and on the following day was presented to that of Burlingham in Norfolk. On the 4th of the ensuing December he was elected, in obedience to a royal mandate, master of his college at Cambridge. In the letter recommending him to the fellows he is described as one, 'as well for his approved learning, wisdom, and honesty, as for his singular grace and industry in bringing up youth in virtue and learning, so apt for the exercise of the said roome, as it is thought very hard to find the like for all respects and purposes' (Strype, Life, i. 28).
In his new capacity Parker exhibited his habitual energy and conscientiousness. He caused inventories of the goods of the college to be made, and enacted a rule for an inspection of the same every three years. Finding the accounts in confusion, he reduced them to order, and directed that they should be annually written out on parchment. A careful inventory of the estates belonging to the society was prepared, with exact statements of their boundaries and rentals. He also, with the assistance of his friend, Dr. William May [q. v.], revised the statutes, and instructed his secretary, John Joscelyn or Josselin [q. v.], to compile the history of the college (Historiola, pp. 38-40).
On 25 Jan. 1544-5 he was elected to the office of vice-chancellor of the university, and on the 25th of the following September was presented by the college to the living of Landbeach in the county of Cambridge. His tenure of office was not unaccompanied with anxiety. The performance at Christ's College of a scandalous play, entitled 'Pammachius,' designed to bring the Roman ceremonial and the papacy into contempt, led to a rigorous inquiry being instituted by Gardiner, then chancellor of the university; Parker unwisely sought to palliate the facts, and his conduct on this occasion lost him the good opinion of Gardiner for the rest of his career. The spoliation with which the colleges generally were threatened in the closing years of Henry's reign was manfully opposed by Parker, who also succeeded in averting for a time the suppression of his college at Stoke. On 16 Jan. 1545-6 he was appointed one of a commission of three to survey the property of all the colleges in the university; and the report which the commission presented to Henry at Hampton Court proved the means of saving the university from further losses for a time. On the sequestration of Stoke College in the following reign, he received a pension of 40l. per annum ; and shortly after (24 June 1547) he married Margaret, the daughter of Robert Harlestone, gentleman, of Mattishall, Norfolk, an ardent, supporter of the reformed doctrines. On 7 Feb. 1548-9 he was again elected vice-chancellor (Correspondence, p. 482).
On the outbreak of Ket's rebellion in 1549 he visited the camp near Norwich, and used his best endeavours to dissuade the rebels from further excesses, although at considerable personal risk. With Martin Bucer [q. v.], who was for a short time regius professor of divinity at Cambridge, Parker lived on terms of closest friendship; was appointed by him one of his executors; and on his friend's death (February 1551) preached his funeral sermon. Throughout the reign of Edward VI Parker continued to grow rapidly in favour with the reformers, and on 7 Oct. 1552 was installed in the rich deanery of Lincoln. On the accession of Mary he was led to espouse the cause of Lady Jane Grey, and was one of a small party who supped with Northumberland when the latter passed through Cambridge on his march for the north. He accordingly found himself completely obnoxious to the authorities in power; the fact of his marriage alone supplying sufficient ground for depriving him of all his prefer-