He took a prominent part in the trial of Fr Thomas Thwing and Mary Pressicks, who were charged on 29 July 1680, at the instigation of the anti-catholic agitators of the day, with compassing the death of King Charles II and seeking the overthrow of the Protestant religion; in his summing up Atkyns placed the case before the jury with becoming impartiality, and Mrs. Pressicks was acquitted, although Fr Thwing was found guilty.
At the close of the same year, he was one of the judges appointed to try William Howard, 1st Viscount Stafford and other Roman Catholic peers on a charge of high treason, but he there supported his colleagues in their contention that the law, which demanded two witnesses to every overt act of treason, might on occasion be waived.
On 21 April 1686, when Lord Chief Baron Montagu was removed from the bench for refusing to certify to the legality of the dispensing power exercised by James II, Atkyns was promoted to his place.
Shortly afterwards Atkyns retired from public life, and withdrew to his country seat at South Pickenham, Norfolk.
[3] Although he continued to hold Jacobite opinions, he showed no bitterness of spirit to those who differed from him, and earned the gratitude of all classes of his neighbours by his tact in settling their disputes.