Writing to Whitgift, archbishop of Canterbury, 20 June 1584, he hotly condemned the archbishop's attempts to prosecute puritan preachers in the court of high commission as unjustly despotic, and treading ‘the highway to the pope’ (Hatfield MSS. iii. 35). He supported Cartwright with equal vehemence. On 24 May 1584 he sent to Burghley a bitter attack on ‘the undermining ambition and covetousness of some of our bishops,’ and on their persecutions of the puritans (ib. pp. 412–13). Repeating his views in July 1586, he urged the banishment of all recusants and the exclusion from public offices of all who married recusants. In 1588 he charged Whitgift with endangering the queen's safety by his popish tyranny, and embodied his accusation in a series of articles which Whitgift characterised as a fond and scandalous syllogism. In the parliament of 1588–9 he vainly endeavoured to pass a bill against non-residence of the clergy and pluralities (Strype, Whitgift, p. 193). In the course of the discussion he denounced the claims of the bishops ‘to keep courts in their own name,’ and denied them any ‘worldly pre-eminence.’ This speech, ‘related by himself’ to Burghley, was published in 1608, together with a letter to Knollys from his friend, the puritan Dr. Reynolds ‘or Rainolds,’ in which Bishop Bancroft's sermon at St. Paul's Cross (9 Feb. 1588–9) was keenly criticised. The volume was entitled ‘Informations, or a Protestation and a Treatise from Scotland … all suggesting the Usurpation of Papal Bishops.’ Knollys's contribution reappeared as ‘Speeches used in the parliament by Sir Francis Knoles,’ in William Stoughton's ‘Assertion for True and Christian Church Policie’ (London, 1642). Throughout 1589 and 1590 he was seeking, in correspondence with Burghley, to convince the latter of the impolicy of adopting Whitgift's theory of the divine right of bishops. On 9 Jan. 1591 he told his correspondent that he marvelled ‘how her Majestie can be persuaded that she is in as much danger of such as are called Purytanes as she is of the Papysts’ (Wright, ii. 417). Finally, on 14 May 1591, he declared that he would prefer to retire from politics and political office rather than cease to express his hostility to the bishops' claims with full freedom.
Knollys's domestic affairs at times caused him anxiety. In spite of his friendly relations with the Earl of Leicester, he did not approve the royal favourite's intrigues with his daughter, Lettice, widow of Walter Devereux, first earl of Essex [q. v.], and he finally insisted on their marriage at Wanstead 21 Sept. 1578. The wayward temper of his grandson, Robert Devereux, second earl of Essex (son of his daughter Lettice by her first husband), was a source of trouble to him in his later years, and the queen seemed inclined to make him responsible for the youth's vagaries. Knollys was created K.G. in 1593, and died 19 July 1596. He was buried at Rotherfield Greys, and an elaborate monument, with effigies of seven sons, six daughters, and his son William's wife, is still standing in the church there. A poem on his death was penned by Thomas Churchyard, under the title ‘A sad and solemne funerall,’ London, 1596, 4to (see reprint in Park's ‘Heliconia’). Two portraits of Knollys and one of his wife are said to have been in possession of a descendant at Fern Hill, near Windsor, in 1776.
Many of his letters are printed in Wright's ‘Queen Elizabeth,’ in the Calendars of the Hatfield MSS., and in Haynes's ‘State Papers.’ Wood states that a manuscript ‘General Survey of the Isle of Wight, with all the Fortresses and Castles near adjoining,’ belonged in his time to Arthur, earl of Anglesey. A manuscript ‘Discourse of Exchange’ by Knollys is at Penshurst (Hist. MSS. Comm. 3rd Rep. p. 230); his ‘arguments against the cross in baptism and the surplice’ are in Lansd. MS. 64, art. 14, and a ‘project’ by him ‘for security of the protestant religion by checking the ecclesiastical power’ is in Lansd. MS. 97, art. 16.
Knollys married Catherine, daughter of William Carey, esquire of the body to Henry VIII, by Mary, daughter of Sir Thomas Boleyn, earl of Wiltshire, and sister of Queen Anne Boleyn. Lady Knollys was thus first cousin to Queen Elizabeth, and sister to Henry Carey, lord Hunsdon [q. v.] She died, aged 39, at Hampton Court, while in attendance on the queen, 15 Jan. 1568–9, and was buried in April in St. Edmund's Chapel in Westminster Abbey, at the royal expense (Hatfield MSS. i. 415). Elizabeth keenly felt her loss (ib. i. 400). A broadside epitaph by Thomas Newton, dated in 1569, belonged to Heber (cf. Bibl. Heber. ed. Collier, p. 55). She left seven sons and four daughters. Of the latter, Lettice (1540–1634) was wife successively of Walter Devereux, earl of Essex, Robert Dudley, earl of Leicester, and of Sir Christopher Blount [see under Dudley, Robert]; Cecilia, maid of honour to Queen Elizabeth, married Sir Thomas Leighton, captain of Guernsey (Nicolas, Hatton, p. 281); Anne, married to Thomas, lord de la Warr; and Catherine, married (1) to Gerald Fitzgerald, lord Offaly, and (2) Sir Philip Boteler of Watton Woodhall.
All Knollys's sons were prominent cour-