His steady attitude of resistance during these years of misgovernment met with recognition at the Revolution. In 1689 he succeeded his brother as chief baron, and in October of the same year, the great seal being in commission, he was appointed speaker of the House of Lords in the place of the Marquis of Halifax. He held the speakership until 1693, and for his services was recommended by the House to the king's favour. Towards the end of the following year he retired from the bench – through disappointment, it has been said, at not being chosen Master of the Rolls, but more likely owing to advancing age. Yet he still gave proof of continued vigour. In a pamphlet published in 1695, and "humbly submitted to the consideration of the House of Lords, to whom it belongeth to keep the inferior courts within their bounds," he renewed Edward Coke's protest against the insidious encroachments of the court of Chancery, tracing the growth of equitable jurisdiction, and suggesting how the common law might be restored. This was followed a few years afterwards by another tract, addressed as a petition to the House of Commons, in which, while repeating his complaint against the court of Chancery, and lamenting the uncertainty of the law, he argued from the history of Parliament that the exercise of judicial functions by the Lords was a usurpation. It should be read along with Skinner's case, in which the Lords failed in their attempt to exercise an original jurisdiction, and Dr. Shirley's case, in which they maintained their right to an appellate jurisdiction. Atkyns had himself, while in parliament, taken a vigorous part in this struggle. After 1699 we hear nothing more of him till his death. He spent his later years at Sapperton Hall in Gloucestershire, and died 18 Feb. 1710, a few weeks before his 90th birthday. Lord Campbell calls him a "virtuous judge," in what was an age of judicial scandals.