With the death of king James, the years of eclipse began. He incurred the enmity of both Buckingham and Laud, and his views and character did not commend him to Charles. On the pretext that he had been appointed on probation, he was deprived of the Great Seal in 1625. The shifts to which he resorted to evade the Star Chamber prosecution initiated by Laud in 1628 were punished in 1637 by a heavy fine, suspension of his ecclesiastical functions, and imprisonment. He remained in the Tower until the Long Parliament met in 1640, when in Nov. the Lords ordered his release and the king sought his advice. It helped to decide Charles to sign Strafford's death-warrant. Yet the historian Gardiner believed that if his counsels had been taken it might also have averted the Civil War (Hist., vi, 340). In 1641 he became archbishop of York.

After his rash action in drawing up the ‘Bishops Remonstrance’ on 30 Dec. 1641, the archbishop found himself again in the Tower. Breaking the conditions on which the Parliament released him in May 1642, he followed the king to Yorkshire, and later in that year fled back to North Wales when the younger Hotham marched against his palace.

There he acted as intermediary between the English and Welsh Royalists and Ormonde in Ireland. At his own cost he repaired and fortified Conway castle, holding the king's written assurance that it should remain in his custody until his outlay was repaid. But owing to his unpalatable advice his influence with the king was waning; and in May 1645 he was unceremoniously turned out of Conway castle by the Royalist, Sir John Owen of Clenennau (q.v.). Convinced that the king's cause was lost, and nursing this grievance, he negotiated with Mytton, commander of the Parliament forces then invading North Wales, and took an active part in his storming of Conway in Aug. 1646.

The Welsh cavaliers never forgave his apostasy, though there are indications that he repented of it after the execution of the king. He d. 25 March 1650 at the Mostyn royalist house of Gloddaeth, and is buried in Llandygài church, near Penrhyn, which he had bought back during his prosperity. Hacket, his biographer, composed the epitaph on his monument; beside it hang Williams's rusted helmet and spurs. He was a good supporter of his college at Cambridge, and it was he who built the beautiful building which houses the library.