In February 1981, in the worst of 3 assassination attempts, his vehicle was attacked with hand grenades and machine gun fire in the center of the capital.

When it became clear that the repression in the countryside was becoming more indiscriminate and, perhaps more importantly, that Ríos Montt was fanatically preaching an evangelical, messianic, born-again type of Christianity, Cerezo withdrew his support for the regime and demanded new elections.

In his inauguration, which was met with great hopes amongst the population, he promised to ensure that what he called the dark forces of the right would not be able to break the public order or the state.

When they failed two days later, with the government refusing to accept the URNG's terms, Cerezo asked the United States for more military aid to further the counter-insurgency efforts of the armed forces.

After a farcical attempt by two colonels to take power on 11 May 1988, on 19 May, an Air Force unit made a series of demands on the government, including breaking ties with pro-USSR countries and stopping any contacts with the URNG, as well as more money for better equipment and the removal of many local politicians.

In August, there was a three-week general strike in protest against the liberalization of petrol and other fuel sources.1989 saw a worsening of the political situation, with 1,600 assassinations and 800 kidnappings or disappearances in the first half of the year.

On 9 May, another attempted coup failed, and though the perpetrators were sentenced to long terms in jail that November, they were released on appeal the following January.

However, on 25 August, Cerezo returned with a new promise to renovate the public administration by consolidating democracy within the 500 days he had left as president.

That same year, as part of a thaw in Soviet–Guatemalan diplomatic relations, Cerezo invited the noted Russian linguist and epigrapher Yuri Knorozov to Guatemala to present him with a medal.

Despite having supported the previous coups that led to human rights abuses in the countryside, President Cerezo claims to have stopped the massacre himself.

He was accused of hiding behind the immunity conferred here and in his role as an ex-president to avoid a variety of charges, including fraud in the buying of a Jordanian island, the covering up of the murder of Myrna Mack Chang, and the concession of a large piece of land to a conservation group owned by Cerezo's son Marco Vinicio Cerezo Blandón.

In the 1999 elections, the unique for which the DCG did not offer a presidential candidate, Cerezo won one of the two National Congress seats gained by his party.

His appointment as Secretary-General of the Central America Integration System (SICA) was announced on 29 June 2017 during the 49th gathering in San Jose, Costa Rica.