In late 1587 in Paris, he was arrested in a brothel, being found in bed with a woman and a male servant of the Earl of Essex. Initially placed in the Bishop's prison, his captors considered sending him back to Walsingham. Eventually he was transferred to the Bastille to await trial. A record of his interrogation shows that he tried to implicate Morgan and Paget in double dealings. In August 1589 he was brought before the court and sentenced to twenty year's imprisonment for acting against the interests of the Catholic Church. At that time Paris was in the control of the Catholic League, which had risen against the French King. While in prison his health deteriorated. At the Battle of Ivry in March 1590 the army of the League was annihilated, and the King marched towards Paris, determined to starve the capital into submission. The siege lasted until August and caused a famine. Gifford died a few months later, in November 1590.