He left the habits for a brief period and entered the Conciliar Seminary of Buenos Aires in 1860. He served as a military chaplain during the Paraguayan War, and for his heroic behavior was promoted to Lieutenant colonel. Canavery was present at the battles of Yatay, Battle of Tuyutí, Battle of Curupayty and Battle of Lomas Valentinas, occurred on December 27, 1868. Finished the war he was added to troops who occupied the city of Asunción. He was the first Chaplain who served in Villa Occidental, being replaced in the position by José Pablo Lynch y Cabrera.