Soon after the outbreak of the Spanish Civil War he became chief of staff to the commander of the Republican Army in the East. In March 1937 Codon was appointed to the position of undersecretary of war. In 1939 Juan Negrin promoted Cordon and other communists such as Juan Modesto and Enrique Lister to senior posts in the army. Segismundo Casado, commander of the Republican Army of the Centre, now became convinced that Negrin was planning a communist coup. On 4th March, Casedo, with the support of the socialist leader, Julián Besteiro and disillusioned anarchist leaders, established an anti-Negrin National Defence Junta.
On 6th March José Miaja in Madrid joined the rebellion by ordering the arrests of Communists in the city. Negrin, about to leave for France, ordered Luis Barceló, commander of the First Corps of the Army of the Centre, to try and regain control of the capital. His troops entered Madrid and there was fierce fighting for several days in the city. Anarchists troops led by Cipriano Mera, managed to defeat the First Corps and Barceló was captured and executed.
Antonio Cordon died in 1965.