In the now-notorious Salem Witch Trials, Stoughton acted as both chief judge and prosecutor. He was particularly harsh on some of the defendants, sending the jury deliberating in the case of Rebecca Nurse back to reconsider its not guilty verdict; after doing so, she was convicted. Many convictions were made because Stoughton permitted the use of spectral evidence, the idea that a demonic vision could only take on the shape or appearance of someone who had made some sort of devilish pact or engaged in witchcraft. Although Cotton Mather argued that this type of evidence was acceptable when making accusations, some judges expressed reservations about its use in judicial proceedings. Stoughton, however, was convinced of its acceptability, and may have influenced other judges to this view. The special court stopped sitting in September 1692.