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 1541 and in 1545–6 attested this grant, making his wife in the second act joint tenant with him. At the same time Francis became one of the gentlemen-pensioners at court, and in 1539 attended Anne of Cleves on her arrival in England. In 1542 he entered the House of Commons for the first time as member for Horsham. At the beginning of Edward VI's reign he accompanied the English army to Scotland, and was knighted by the commander-in-chief, the Duke of Somerset, at the camp at Roxburgh, 28 Sept. 1547 (, Lit. Rem. of Edw. VI, ii. 219). Knollys's strong protestant convictions recommended him to the young king and to his sister the Princess Elizabeth, and he spent much time at court, taking a prominent part not only in tournaments there (ib. ii. 389), but also in religious discussion. On 25 Nov. 1551 he was present at Sir William Cecil's house, at a conference between a few catholics and protestants respecting the corporeal presence in the Sacrament (, Cranmer, 1848, ii. 356). About the same date he was granted the manors of Caversham in Oxfordshire and Cholsey in Berkshire. At the end of 1552 he visited Ireland on public business.

The accession of Mary darkened Knollys's prospects. His religious opinions placed him in opposition to the government, and he deemed it prudent to cross to Germany. On his departure the Princess Elizabeth wrote to his wife a sympathetic note, expressing a wish that they would soon be able to return in safety (, Letters of Illustrious Ladies, iii. 278–9). Knollys first took up his residence in Frankfort, where he was admitted a church-member, 21 Dec. 1557, but afterwards removed to Strasburg. According to Fuller, he ‘bountifully communicated to the necessities’ of his fellow-exiles in Germany (Church Hist. iv. 228), and at Strasburg he seems to have been on intimate terms with Jewel and Peter Martyr (cf., Reformation, iii. 500). Before Mary's death he returned to England, and as a man ‘of assured understanding and truth, and well affected to the protestant religion,’ he was admitted to Elizabeth's privy council in December 1558 (, Annals, p. 12). He was soon afterwards made vice-chamberlain of the household and captain of the halberdiers, while his wife and her sister—first cousins of Elizabeth—became women of the queen's privy chamber (Hatfield MSS. i. 158). In 1560 Knollys's wife and son Robert were granted for their lives the manor of Taunton, part of the property of the see of Winchester. In 1559 Knollys was chosen M.P. for Arundel, and in 1562 for Oxford, of which town he was also appointed chief steward. In 1572 he was elected member for Oxfordshire, and sat for that constituency until his death. Throughout his parliamentary career he was a frequent spokesman for the government on questions of general politics, but in ecclesiastical matters he preserved as a zealous puritan an independent attitude.

Knollys's friendship with the queen and Cecil led to his employment in many offices of anxious responsibility. In 1563 he was governor of Portsmouth, and was much harassed in August by the difficulties of supplying the needs in men and money of the Earl of Warwick, who was engaged on his disastrous expedition to Havre (see ; Hatfield MSS. i. 274–5). In April 1566 he was sent to Ireland to control the expenditure of Sir Henry Sidney, the lord deputy, who was trying to repress the rebellion of Shane O'Neil, and was much hampered by the interference of court factions at home; but Knollys found himself compelled, contrary to Elizabeth's wish, to approve Sidney's plans. It was, he explained, out of the question to conduct the campaign against the Irish rebels on strictly economical lines (cf., Ireland under the Tudors, ii. 105–7). In August 1564 he accompanied the queen to Cambridge, and was created M.A. Two years later he went to Oxford, also with his sovereign, and received a like distinction there. In the same year (1566) he was appointed treasurer of the queen's chamber.

In May 1568 Mary Queen of Scots fled to England, and flung herself on Elizabeth's protection. She had found refuge in Carlisle Castle, and the delicate duty of taking charge of the fugitive was entrusted jointly to Knollys and to Henry Scrope, ninth baron Scrope. On 28 May Knollys arrived at the castle, and was admitted to Mary's presence. At his first interview he was conscious of Mary's powerful fascination. But to her requests for an interview with Elizabeth, and for help to regain her throne, he returned the evasive answers which Elizabeth's advisers had suggested to him, and he frankly drew her attention to the suspicions in which Darnley's murder involved her. A month passed, and no decision was reached in London respecting Mary's future. On 13 July Knollys contrived to remove her, despite ‘her tragical demonstrations,’ to Bolton Castle, the seat of Lord Scrope, where he tried to amuse her by teaching her to write and speak English (Hatfield MSS. i. 400). Knollys's position grew more and more distasteful, and writing on 16 July to Cecil, whom he kept well informed of Mary's conversation and