In early 1811 Father Barona was transferred to Mission San Juan Capistrano, registering his first baptism at that station on April 26. In 1826 Father Barona refused to take the oath of allegiance to the "bogus republic of Mexico" despite the fact that he (along with all of the other Spanish missionaries) had previously sworn to the Independence of Mexico; then Governor José María de Echeandía nevertheless recommended that Barona not be deported when the law of December 20, 1827 (requiring the expulsion of all Spaniards younger than sixty years of age) took effect in California. José Barona remained at San Juan Capistrano, where he ministered to the natives until his death on August 4, 1831. Barona's remains were subsequently interred beneath the floor of the "Great Stone Church," where they rest beside the remains of Fathers Vicente Fustér and Vicente Pascual Oliva.