Against a background of strikes and civil unrest, factions within the military rebelled in 1955, with the tacit support of a broad coalition of those interests that Perón had alienated, including the Church and the oligarchy. In the Revolución Libertadora , or Revolution of Liberation, he was ousted from power and went into exile, to the delight of his enemies. The initial backlash against Peronism was swift and stinging: General Aramburu banned it as a political movement, Peronist iconography and statues were stripped from public places, and even mention of his name was forbidden. There followed eighteen years of alternate military and short-lived civilian regimes like those of the Radicals Arturo Frondizi and Arturo Illia that lurched from one crisis to another with little in the way of effectual long-term policies. Civilian administrations were dependent on the backing of the military, which itself was unsure of how to align itself with the Peronist legacy and the trade unions. Much of the 1960s was characterized by economic stagnation, strikes, wage freezes and a growing disillusionment of the populace with the institutions of government. Throughout this time, Perón hovered in the background, in exile in Spain, cultivating dissidence amongst the trade unions, and providing a focus for opposition to the military.

In 1966, a military coup led by General Juan Carlos Onganía saw the imposition of austere measures to stabilize the economy, and repression to keep a tight reign on political dissent. This was not without consequences, and, in the city of radical politics, Córdoba, tension eventually exploded into violence in May 1969. In what has become known as the Cordobazo , left-wing student protesters and car-worker trade unionists sparked off a spree of general rioting that lasted for two days, left many people dead, and the authorities profoundly shaken. Onganía's position was becoming less and less tenable and, with unrest spreading throughout the country and an economic crisis that provoked devaluation, he was deposed by the army.

It was about this time that society saw the emergence of guerrilla organizations, which crystallized, over the course of the early 1970s, into two main groups: the People's Revolutionary Army (Ejército Revolucionario del Pueblo or ERP ), which was a movement committed to radical international revolution in the style of Trotsky or Che Guevara; and the Montoneros , which was a more urban movement that espoused revolution on a more distinctly national model, extrapolated from left-wing traits within Peronism. Multinationals, landed oligarchies and the security forces were favoured Montonero targets.