Whitgift confidentially informed Dr. Neville, master of Trinity, that the articles must not be formally published owing to the queen's dislike of them. He had only intended to let the Cambridge Calvinists know that ‘he did concur with them in judgment and would to the end, and meant not to suffer any man to impugn [those opinions] openly or otherwise.’ There the matter was allowed to drop. For the remaining years of the queen's reign Whitgift mainly confined his attention to administrative reforms. Order was taken to secure a higher standard of learning among the inferior clergy (Wilkins, Concilia, iv. 321; Cardwell, Synodalia, ii. 562), and canons were passed in 1597 to prevent the abuse of non-residence. It is said by his biographer Paule that he sought a reconciliation with Cartwright. But Whitgift still fought hard for the independence of ecclesiastical courts, and, while revising their procedure, he protested in 1600 against the growing practice in the secular courts of law of granting ‘prohibitions’ suspending the ordinances of the court of high commission.
On the occasion of Essex's rebellion in January 1600–1, Whitgift, despite his personal friendship for the earl, who was his old pupil, showed the utmost activity in anticipating an attack on the queen. He sent from Lambeth a small army of forty horsemen and forty footmen to protect the court in case of need. The archbishop's troop of footmen secured Essex's arrest at Essex House, and conducted him to Lambeth before carrying him to the Tower. Whitgift attended Queen Elizabeth during her last illness, and was at her bedside when she died at Richmond on 23 March 1602–3. He acted as chief mourner at her funeral in Westminster Abbey. Meanwhile he was not neglectful of his relations with her successor. He attended the council at which James VI of Scotland was proclaimed king, and at once sent Thomas Neville, dean of Canterbury, to Edinburgh to convey his congratulations. He employed terms of obsequiousness which have exposed him to adverse criticism, but he was merely following the forms in vogue in addressing sovereigns. At the king's invitation he forwarded a report on the state of the church, and received satisfactory assurances that the king would prove his fidelity to the Anglican establishment. In May Whitgift met the king for the first time at Theobalds on his way to London, and on 25 July celebrated his coronation. The puritans hoped for new liberty from the new régime, and Whitgift found himself compelled to adopt the king's suggestion of a conference with the puritan clergy, in order that the points of difference between them might be distinctly stated. The conference was opened at Hampton Court on 16 Jan. 1603–4. The king presided. Whitgift attended as the veteran champion of orthodoxy, but it was left to Richard Bancroft, bishop of London, to take the leading part in the discussions. The archbishop was placed in an embarrassing position by the importunity of John Rainoldes, the leader of the puritan disputants, in urging the formal adoption by the heads of the church of Whitgift's Lambeth articles. James I finally decided the main points in the bishops' favour.
Whitgift was feeling the inconveniences of old age. In February 1604 he caught cold while travelling on his barge from Lambeth to the bishop of London's residence at Fulham to consult with the bishops on church business. A few days later—the first Sunday in Lent—he went to dine at Whitehall, and while at dinner was stricken with paralysis. He was removed to Lambeth. The king paid him a visit a few days later, but his power of speech was gone. He could only ejaculate at intervals the words ‘Pro ecclesia Dei.’ He died—‘like a lamb,’ according to his attendant and biographer, Paule—on 29 Feb. 1603–4. The next day his body was carried to Croydon, and his funeral was solemnised there on 27 March 1604 in great state. A sermon was preached by Gervase Babington, bishop of Worcester. In the south-east corner of the chantry of St. Nicholas in the parish church of Croydon there was set up a monument on which lay his recumbent effigy, with his hands in the act of prayer; the decoration included his armorial bearings as well as those of the sees of Canterbury and Worcester, the deanery of Lincoln, and the colleges of Peterhouse, Pembroke Hall, and Trinity, at Cambridge. The monument was much injured in the fire which nearly destroyed the church on 5 Jan. 1867. Thomas Churchyard [q. v.] issued on Whitgift's death a poem called ‘Churchyards Good Will, sad and heavy Verses in the nature of an Epitaph’ (London, 1604, 4to; reprinted in Park's ‘Heliconia,’ vol. iii.) Another ‘epitaph’ in the form of a pamphlet appeared anonymously in the same year from the pen of John Rhodes, and a eulogistic life by the controller of his household, Sir George Paule [q. v.], was published in 1612.
With his contemporaries Whitgift's character stood very high, in spite of the rancour with which he was pursued by puritan pamphleteers. The poet Thomas
