During the Spanish Civil War (1936–39) he was briefly in charge of Supplies for the Madrid Defense Council, before being shot and badly wounded at an Anarchist roadblock.

[1] In 1930 he joined the Communist Party of Spain (Partido Comunista de España, PCE) along with other union leaders such as Isidoro Diéguez and Luis Cabo Giorla.

The communists were given three ministries, War, Supplies and Public Order, which were to be led by Antonio Mije, Pablo Yagüe and Santiago Carrillo, respectively.

[11] Those involved, who were arrested after the incident by forces of Santiago Carrillo's Delegation of Public Order, were eventually acquitted by a people's court.

[12] Due to the severity of his wounds, Yagüe was relieved as a member of the Council and replaced by Luis Nieto de la Fuente, his deputy.

[1] Yagüe was in Porlier prison when Madrid fell into the hands of General Francisco Franco's troops, resulting in the end of the civil war.

[16] He hid in the house of Alicia Martinez, whom he had known during the civil war and with whom he had a relationship, without getting involved in rebuilding the clandestine structure of the party.

[19] Yagüe, with eleven of the accused, was sentenced to death and shot by firing squad on 19 May 1943 against the walls of the Cementerio de la Almudena.