He was in Évora in 1807, setting up courses in ecclesiastical history, Biblical theology, polemics, and morals, when these were interrupted by the Napoleonic invasion of Portugal in the context of the Peninsular War. As the Portuguese revolted against the French occupying forces, Évora's poorly-armed townsmen and militias were slaughtered in a short battle in July 1808 and the city was brutally sacked by the troops of Louis Henri Loison. Archbishop Manuel do Cenáculo, at that point aged 85, refused Spanish colonel Frederico Moretti's suggestion to flee the city as it became apparent the French forces had won the battle; as the troops stormed the Cathedral (shooting a chaplain, and throwing grenades that killed several people gathering there), the Archbishop rose from the cathedra and, held at bayonet point, humbly capitulated, begging them to spare the lives of his flock. After seeing the Archepiscopal Palace occupied and sacked, especially his natural history museum and his library, and between violent threats and insults, Manuel do Cenáculo was arrested by the French and carried to prison in Beja, where he remained without recognising the authority of the new regency.