From 1843 to 1846, Mouton was governor of Louisiana. As governor, Mouton reduced expenditures and liquidated state assets to balance the budget and meet bond obligations without raising taxes. He sold state-owned steamboats, equipment and slaves used to remove the Red River Raft in 1834 under Governor Roman. As governor, he opposed all expenditures for internal improvements. He leased out state penitentiary labor and equipment. He supported the call for a constitutional convention, removal of property qualifications for suffrage and office holding, and the election of all local officials and most judges.