Born on March 7, 1891, in Zamora, Michoacán to a Liberal trading family, Magaña was sent to study economics in the United States at the Temple College in Pennsylvania.

Back in Mexico he was involved in the anti-reelectionist movement and had to flee to the insurrectionist Zapatista country people in Morelos in 1911.

He was immediately made use of as emissary to various revolutionaries in different parts of Mexico, among others to Pancho Villa whom he is reported to have taught reading.

In 1916 he was appointed chief of staff to Emiliano Zapata, because he was the only one who was able to make unruly sub-commanders of the movement cooperate instead of quarrel, using his personal charm as well as his outstanding diplomatic skill for the task.

In November 1919, due to the international conflict with the United States caused by the kidnapping of Consul Jenkins,Magaña and other southern chiefs accepted the amnesty of Venustiano Carranza's government, thinking of putting himself in defense of the nation that was threatened by a North American invasion.In January 1920 he took up arms again, probably at the suggestion of Álvaro Obregón and shortly after it joined the Plan of Agua Prieta.