Uncharismatic but tenacious, Ovando was bidding his time, counting on the fact that he would be the logical choice to run for elections once Barrientos' term ended in 1970, perhaps with some electoral "help" from the outgoing administration. Soon, major differences emerged between Ovando and the president, however, especially in regard to the massacre of miners at Siglo XX in June of 1967, and the so called Arguedas Affair of 1968. In early 1967, a guerrilla force had been discovered to be operating in the rural Bolivian southwest under the leadership of the Argentine - Cuban revolutionary Ernesto "Che" Guevara. While the insurgency was eventually put down by Bolivian military troops (with various disputed degrees of American help) and Guevara was captured and executed in October of 1967, the event fostered a major spin - off scandal that eruped in 1968. That year, Barrientos' trusted friend and Minister of Interior, Antonio Arguedas, disappeared with the captured diary of Che Guevara, which soon surfaced in, of all places, Havana. From abroad, Arguedas confessed himself to have been all along a clandestine Marxist supporter, and denounced Barrientos and many of his aides as being on the CIA's payroll. This event embarrassed Barrientos since it reflected poorly on his choices, and prompted Ovando to distance himself from the president with an eye to the projected 1970 elections.

The worries proved unnecessary, for Barrientos perished in a tragic helicopter crash on April 27, 1969. His Vice - President, a little known Christian Democrat politician named Luis Adolfo Siles, was sworn as President soon thereafter, in accordance to the Constitution. Siles' poor relations with Ovando led Siles to support the candidacy of the popular Mayor of La Paz, Armando Escobar, as the true successor of the now constantly eulogized Barrientos, threatening to spoil the carefully laid plans of Ovando.

Furthermore, Ovando had been undergoing a political metamorphosis, and had come to conclude that he had to move to the Left in order to be acceptable as President in the ideologically super - charged atmosphere of the late 1960s. The changes he planned to institute could be difficult to enact in the presence of a potentially hostile Congress. For these reasons, Ovando decided not to wait for the elections (which no one could guarantee he could win, with the popular Escobar as candidate) and on September 26, 1969, he executed a coup d'état that overthrew Siles.

Ovando's short (13 month) dictatorship was difficult and marked by political violence. Upon taking office, he declared himself in favor of fundamental changes aimed at enhancing the deplorable living conditions of the vast majority of Bolivians. To this end, he nationalized the Bolivian operations of the U.S. based Gulf Oil Corporation and called on known leftist intellectuals to become part of his cabinet. Ovando also announced his political adherence to the principles espoused by other so-called "leftist military" regimes then in vogue in Latin America, foremost of which were the regimes of Peru's Juan Velasco and Panama's Omar Torrijos.

Ovando's populist stance surprised many conservative members of the Bolivian military and failed to fully satisfy the increasingly more belligerent forces of the Left, especially the workers and students. Worse, the military (in whose name he served) had become polarized, with some sectors supporting the President and even calling for a further leftward turn (General Juan José Torres) and others criticizing Ovando and urging a more conservative, anti - Communist, and pro U.S. stance (General Rogelio Miranda). In June 1970, a new Marxist guerrilla emerged in the lowlands near La Paz, this time constituted mostly by Bolivian university students aligned with the outlawed Ejército de Liberación Nacional (National Liberation Army, or ELN). The new guerrilla outbreak was easily controlled, but Ovando's response had been rather vacillating and timid. He offered a generous safe haven to guerrillas who gave up the fight, for example, in contrast to Barrientos' call for "heads on spikes" in 1967. The forces of the right had had enough.

On October 6, 1970, an anti - government coup d'état took place via a junta of commanders of the Bolivian Military. However, the polarized forces of the military were evenly split. Much blood was shed on the streets of various major cities, with garrisons fighting each other on behalf of one camp or the other. Eventually, President Ovando sought asylum in a foreign embassy, believing all hope was lost. But the leftist military forces re-asserted themselves under the combative leadership of General Juan José Torres, and eventually triumphed. Embarrassed by his quick abandonment of the fight, and worn out by 13 grueling months in office, Ovando agreed to leave the presidency in the hands of his friend, General Torres. The latter was sworn in and rewarded Ovando with the Bolivian ambassadorship in Spain. Ovando remained in Madrid until 1978, when he returned to Bolivia. In his latter years, he supported the progressive UDP alliance of former President Hernán Siles, but otherwise never participated in active politics again.

He died in La Paz on January 4, 1982.