Shortly after beginning his term as a congressman in 2009, Duarte de Ochoa began to be mentioned as one of the major PRI candidates for Governor of Veracruz in the 2010 elections. His candidacy received support from the Confederación Nacional Campesina and the Confederación de Trabajadores de México, and he was designated PRI candidate for the governorship on 27 March 2010.
The governor's race for the 2010 State Elections of Veracruz was between Javier Duarte de Ochoa of the PRI, Miguel Ángel Yunes Linares of the PAN and the incumbent Dante Delgado Rannauro, who had been elected by a coalition between the PRD, PT and Convergence. When voting closed on 2 July 2010 Duarte de Ochoa was originally declared winner with 50% of the votes, with only 36% for the closest contender Dante Delgado Rannauro. However, accusations of suspicious votes and rampant fraud led the opposition parties to file a formal request for an investigation and vote-by-vote recount, which was accepted by the PRI on 8 July 2010. Duarte de Ochoa had received a record number of votes, with over 79,000 more than the incumbent Dante Delgado Rannauro had received in the previous election, and telephone recordings were revealed in which former PRI governor and Duarte de Ochoa supporter Fidel Herrera Beltrán was heard pledging to use state resources to support the Duarte de Ochoa campaign. However, although the Election Tribunal annulled 260 voting boxes, bringing the margin of the win to just 2%, they claimed that the opposition had not presented sufficient proof to annul the election, and Duarte de Ochoa was declared the victor on 26 July 2010.
In September 2011, 35 bodies were found tortured and murdered in two abandoned trucks in the town of Boca del Rio, Veracruz, outside a building where governor Duarte de Ochoa was conducting a meeting. As evidence emerged that the killings had been made possible through police collusion, the governor took the unprecedented step of disbanding the entire Boca del Rio police force in an attempt to root out corruption.
In March 2017 an estimated 250 human remains were found in mass graves in Veracruz
On Friday 28 January 2012 members of the Federal Police arrested Said Zepeda and Miguel Morales, who were carrying a briefcase and a backpack with cash totalling 25 million pesos (nearly US$2 million at that time) on an official Veracruz state government plane with unverified origin or destination, and which was suspected of being sent for unlawful purposes by the Duarte de Ochoa government. The cash was seized and a federal investigation was launched to determine whether the source of the money was legitimate, and if it indeed belonged to the state government of Veracruz. Finance Secretary Tomás Ruiz González claimed that in spite of the odd mode of transportation, the money was legal and intended to pay for the advertisement of local festivals. The federal investigation eventually found no evidence for illegal activity, and the cash was returned to the Veracruz government on 5 June 2015 with interest.
Since Duarte de Ochoa took office in December 2010, his tenure has seen a number of cases of local journalists under threat.
Duarte has issued numerous threats to journalists in several interviews. As of 1 August 2015, twelve journalists and crime reporters have been killed during the tenure of Duarte de Ochoa, and three more have gone missing Most of the cases have gone unsolved. The most notorious case was that of journalist Regina Martínez Pérez, widely known for her reporting on Veracruz state corruption and its links to drug cartels, who was found strangled to death in her apartment on 28 April 2012. State officials claimed her murder was unrelated to the regular threats of violence she was receiving for her reporting, but was rather a crime of passion following a robbery, and on 9 April they sentenced Jorge Antonio Hernández Silva to 38 years in prison for the murder.
Due to the unprecedented number of journalist killings during Duarte de Ochoa's term as governor, the international association Reporters Without Borders named the state of Veracruz one of the ten most dangerous places in the world in which to practice journalism.
After being hit by a wave of corruption scandals and the loss of his PRI membership, Duarte presented his resignation to the Veracruz state legislature on 12 October 2016 and made his last public appearance the next day, leaving his whereabouts unknown from that date until his arrest on 15 April 2017. He was replaced by an interim appointment, Flavino Ríos Alvarado, who will serve the 48 days between Duarte's resignation and the installation of Miguel Ángel Yunes as the next governor. On March 12, 2017, Veracruz authorities arrested Ríos, accusing him of aiding Duarte's escape and abusing his authority; a judge delivered a cautionary one-year jail sentence.
The federal Attorney General filed organized crime charges on Duarte on 17 October 2016. The PRI expelled Duarte from the political party and issued an apology. His whereabouts were unknown and the government through the "Procuraduria General de la Republica" offered a reward of $15 million pesos for information that could help towards his capture. Duarte Ochoa was subsequently arrested in Guatemala on 15 April 2017. He was extradited from Guatemala to Mexico on July 17, 2017.