Wakeman was indicted for high treason at the Old Bailey on 18 July 1679, together with three priests, the case being tried by Lord Chief Justice William Scroggs, assisted by his fellow Chief Justice Francis North, 1st Baron Guilford and the junior King's Bench judges. Scroggs, formerly a strong believer in the Popish Plot, was on this occasion, for reasons which have never been entirely clear, firmly on the side of the accused. The chief witnesses for the prosecution were William Bedloe and Oates, who swore that he had seen the paper appointing Wakeman to the post of physician-general. It was elicited from Oates in the course of the proceedings that he was incapable at the time alluded to of identifying either Wakeman's person or his handwriting. Wakeman and his co-accused all defended themselves with great vigour (in a case of treason the accused was not entitled to counsel until the passage of the Treason Act 1695), and their witnesses received a far more courteous hearing than defence witnesses in previous trials had. In particular Ellen Rigby, the housekeeper to the Benedictine order in London, was listened to with a respect not often accorded to a Catholic woman in that age. Scroggs in his summing up commented severely upon the character of the evidence, stressed his reluctance to shed innocent blood, (a reluctance which had certainly not been evident in previous Plot trials), and warned the jury that while he still believed in the Plot, it must not be assumed that all those accused were party to it. The jury, after asking if they might find the prisoners guilty of misprision of treason, and being told they could not, found all the prisoners not guilty.