On 13 April 1796, Willot transferred to the "Army of Rhin-et-Moselle". He took command of the 8th Military Division on 25 July the same year. This was in Marseilles where he claimed to be impartial but managed to offend the Jacobin party. Napoleon Bonaparte was influential in getting him removed. At this time he joined the Royalist faction. Evidently, his political leanings were well known because Pierre Augereau blustered that Willot in Marseilles had nearly sabotaged the Battle of Arcole campaign by failing to reinforce the "Army of Italy". Willot was elected to the Council of Five Hundred on 11 April 1797. He was elected for the Bouches-du-Rhône by 102 out of 203 votes. He became the Council's Secretary and later Inspector.