With the later outbreak of the insurrection under Father Miguel Hidalgo in September 1810, Michelena was again arrested. He was held a prisoner in San Juan de Ulúa (Veracruz) until 1813, after which he was sent to Spain. He contracted a severe case of rheumatism in the prison. In Spain, he joined a military unit fighting the French. He was involved in numerous actions, including the capture of Bayonne in February 1814.