During the Spanish Civil War, Arrue drew comics describing events from the perspective of the Basque Government. After the collapse of the Republican Army of the North, and the fall of Santander on September 1, 1937, Arrue was arrested in the city. He was held in Nationalist captivity for two years, during which time he was moved to Orduña prison. He was eventually released in 1940 and went to live in Llodio with his family. Although in semi-retirement from public life, he participated in a number of further exhibitions: a retrospective of his work was held in 1973, and a further one, featuring the work of all of the Arrue brothers, was held in Bilbao in 1977.