On 20 July 1685, a fortnight after the Battle of Sedgemoor, the old lady consented to shelter John Hickes, a well-known Nonconformist minister, at her residence, Moyles Court, near Ringwood. Hickes, who was a fugitive belonging to Monmouth's army, brought with him Richard Nelthorpe, also a partizan of Monmouth, and under sentence of outlawry. The two men passed the night at Moyles Court, and on the following morning were arrested, and their hostess, who had denied their presence in the house, was charged with harbouring traitors.
Her case was tried by Judge Jeffreys at the opening of the Bloody Assizes at Winchester. She pleaded that she had no knowledge that Hickes's offence was anything more serious than illegal preaching, that she had known nothing previously of Nelthorpe (whose name was not included in the indictment, but was, nevertheless, mentioned to strengthen the case for the Crown), and that she had no sympathy with the rebellion. The jury reluctantly found her guilty, and, the law recognizing no distinction between principals and accessories in treason, she was sentenced to be burned.
Jeffreys ordered that the sentence should be carried out that same afternoon, but a few days' respite was subsequently granted, and James II allowed beheading to be substituted for burning. Lady Lisle was executed in Winchester market-place on 2 September 1685. She is buried in a tomb on the right hand side of the porch at St Mary's church, Ellingham, Hampshire. There is a plaque marking the spot of Lady Lisle's execution opposite "The Eclipse Inn" near the Cathedral in Winchester.By many writers her death has been termed a judicial murder, and one of the first acts of parliament of William and Mary reversed the attainder on the ground that the prosecution was irregular and the verdict injuriously extorted by "the menaces and violences and other illegal practices" of Jeffreys. It is, however, extremely doubtful whether Jeffreys, for all his gross brutality, exceeded the strict letter of the existing law.