The Guatemalan military dictators of the mid-to-late 20th century were noted for their cruelty, corruption and appetite for power. Gen Efraín Ríos Montt, who has died aged 91, added an extra ingredient to the mix: he was a Protestant fundamentalist with a mission to save the country – even the continent – for Jesus.

“A Christian should carry his bible and his machine-gun,” he once remarked. He put his own preachings into practice with a counter-insurgency campaign that killed thousands and wiped hundreds of villages from the map during his 1982-83 de facto government.

Born in Huehuetenango, in the western highlands, Ríos Montt had joined the army 40 years earlier, just before the overthrow of the dictator Jorge Ubico ushered in a decade of democratic and social reforms. Unfortunately, Washington and the United Fruit Company (a US transnational whose interests were affected by the reforms) found dictatorship more to their liking, and in 1954 they sponsored a rightwing military coup that banished democracy for more than 30 years.

Like many of his fellow Latin American dictators, Ríos Montt benefited from US training – in his case at Fort Gulick, in the Panama Canal Zone, and Fort Bragg, North Carolina. He also attended the Army School of War in Italy. In later years he would be appointed military attaché in the Guatemalan embassy in Washington and Guatemalan representative on the Inter-American Defense Board.

Under the government of Gen Carlos Arana (1970-74), he became army chief of staff. But he resigned his commission in 1974 to stand as presidential candidate for the National Opposition Front (FNO), an electoral alliance formed around the Christian Democrat Party (DCG).

Facebook Twitter Pinterest Ríos Montt on trial in 2013. His conviction and 80-year jail sentence were later overturned. Photograph: ZUMA/Rex/Shutterstock

The military regime, however, was not yet willing to contemplate handing over power, even to one of its own. Ríos Montt was cheated of what was widely believed to have been a victory and the official candidate, Gen Kjell Laugerud, declared the winner. Lest he become the focus of a protest movement, the government quickly restored the unlucky loser to active service and posted him as military attaché to Madrid, where he remained until 1978. Two years before his return, after the devastating 1976 earthquake, an evangelical Protestant missionary group from Eureka, California, called Gospel Outreach had moved into Guatemala. On his return to the country, Ríos Montt rapidly became a convert and was soon a leading member of its local branch, known as El Verbo (The Word).

Believers in the literal truth of the Bible, the Gospel Outreach missionaries were bent on nothing less than the conversion of the Americas. In common with other fundamentalist groups they were fiercely anti-communist, and they were to prove a useful ally for the general in his campaign to wipe out “subversion” in the form of the leftist Guatemalan National Revolutionary Unity (URNG) guerrilla front and its civilian followers.

In March 1982, young officers led a reformist coup to forestall the installation in the presidential palace of yet another dictator, Gen Aníbal Guevara. Ríos Montt was invited to take part in a three-man ruling junta, which promptly annulled the constitution, banned political parties and dissolved congress. The US ambassador exulted that: “Guatemala has come out of the darkness into the light.” Appointing himself president and defence minister, and ruling by decree after declaring a “state of siege”, Ríos Montt declared that he would, “moralise national life from the top down”.

His morality campaign included executions by firing squad, which earned him a rebuke from the Vatican, among others. But his brief presidency was most notorious for the scorched-earth policy he adopted towards the highland indigenous communities where support for the URNG was strongest.

Under plans known as Victory 82 and Guns and Beans, the country’s Mayan population was seen as an “internal enemy” of the state, and the army was sent to destroy villages suspected of harbouring guerrilla sympathisers. About 440 villages were razed to the ground. Men, women and children were systematically massacred and the survivors herded into strategic hamlets and indoctrinated against “communism”. Their sacred sites were violated and their culture, religion and language suppressed.

As many as 10,000 are thought to have been killed, while tens of thousands more fled across the border into Mexico, or hid for years in the mountains.

A vast network of civilian self-defence patrols (PACs) was set up, in some cases led by members of El Verbo, who also helped identify alleged guerrilla sympathisers. All of this endeared the general to the fundamentalist right in the US: he received support from the likes of Pat Robertson and Jerry Falwell. Ronald Reagan, who took a particular liking to him, declared he had had a “bum rap”’ on human rights.

In August 1983, however, the army high command finally tired of being ordered around by a maverick evangelical general and toppled Ríos Montt’s government. But this was by no means the end of his political career. As democracy was gradually restored, beginning with the 1986 elections, the general refashioned himself as a civilian politician, founding a party of his own – the Guatemalan Republican Front (FRG) – and seeking election to the presidency.

The 1985 constitution, however, bars the leaders of coups d’etat from holding the presidency, and Ríos Montt’s attempt to have the ban overturned by the Inter-American Commission on Human Rights failed to prosper. Nonetheless, the FRG grew in strength, and in the 1999 elections its candidate, Alfonso Portillo, was elected president.

Despite charges of genocide, laid before the Spanish Audiencia Nacional by Nobel peace prize-winner Rigoberta Menchú, Ríos Montt became president of congress in May 2000. He frequently denied not only giving orders for massacres or a scorched earth policy but even receiving reports of such atrocities committed by the army. Whatever his other peculiarities, in that respect Ríos Montt was just a run-of-the-mill tyrant.

As a member of congress the former dictator enjoyed legal immunity, but that ran out when his final parliamentary term expired in 2012. The following year he was convicted of genocide and crimes against humanity by a Guatemalan judge who sentenced him to 80 years’ imprisonment. The case centred on successive massacres in the so-called Ixil triangle of El Quiché department, which took the lives of almost 1,800 indigenous men, women and children. The conviction was later overturned, although a retrial was under way when the general died.

He is survived by his wife, María Teresa Sosa, a daughter, Zury, a politician, and a son, Enrique, who was a soldier and served as defence minister. Another son, Adolfo, also joined the army, participated in his father’s coup and was killed in 1984 in a rebel downing of a military helicopter.

• José Efraín Ríos Montt, military leader and politician, born 16 June 1926; died 1 April 2018