In 1945, also with support of the military junta in power at that time, Alonso founded the FONIVA (Federación Obrera Nacional de la Industria del Vestido, National Workers' Federation of the Clothing Industry), and became its vice-secretary.
He travelled abroad, being delegate of Argentine workers' in several conferences of the International Labour Organization (ILO) and took part in the formation of the ATLAS (Agrupación de Trabajadores Latinoamericanos Sindicalistas, a Latin American trade-union confederation) in 1952.
José Alonso then participated, along with other unionist leaders, as representative of the CGT, to the first National Congress of Philosophy, held in Mendoza in March–April 1949, which contributed to set the bases of the Peronist movement.
Alonso became a member of the "Commission of the 20", a unionist organization which gathered Peronists and independents, and headed the CGT following its legalization by Frondizi's government on February 28, 1961.
One hundred trade unions participated, and because the 62 Organizations supported José Alonso as candidate for Secretary General of the CGT, he was thus elected on February 1, 1963.
But on December 4, 1963, he presented a 15 points petition list, which requested increased wages, rupture with the International Monetary Fund (IMF), active participation of workers' in the state firms and the elimination of unemployment.
Meanwhile, the government and the military supported internal struggles among the CGT, particularly following Labor Minister Rubens San Sebastián's implementation of a "divide and conquer" policy, around 1966.
Despite open support from Perón and his wife, José Alonso lost his functions at the CGT on 2 February 1966, under pressure from the Vandoristas, and was replaced by Fernando Donaires.
Using his effective diplomatic relationship with the Roman Catholic Church in Argentina and the Armed Forces, he supported a coup d'État against Arturo Illia's elected government, and managed to reach an agreement with Vandor, both unified in common criticisms of liberal democracy.
[1] Following Juan Carlos Onganía's military coup of June 28, 1966, Alonso declared: "We congratulate ourselves in having witnessed the fall of the last bourgeois liberal government, because it will never be able to establish itself here again.".
Along with Rogelio Coria, José Alonso participated to the Nueva Corriente de Opinión, which, headed by Taccone, supported a "participationist" or "collaborationist" attitude toward the military regime.
A new tendency, opposed to the latter, formed in the workers' movement, headed by Amado Olmos, Raimundo Ongaro, Julio Guillán, Jorge Di Pasquale, Ricardo De Luca, Atilio Santillán, and Agustín Tosco.