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Honduran President, Manuel Zelaya came from a wealthy, land-owning background, was elected as a traditional neoliberal in 2006, and then shifted toward the political left during his presidency.

During his term (2006-2009), Zelaya surprised many of his traditional elite supporters by shifting toward left-of-center policies. This included increasing the minimum wage by 80%, providing subsidies to small farmers, and aligning Honduras with the Bolivarian Alliance for the Americas (ALBA), an organization promoted by Venezuela's then-leftist President Hugo Chávez. This shift lost him the support of the Honduran business elites, the military, the judiciary, and many members of his own party.

On June 28, 2009, the Honduran military stormed the presidential palace, arrested President Zelaya (reportedly while he was still in his pajamas), and forcibly exiled him by putting him on a plane to Costa Rica. The Honduran Congress then officially voted to remove him from office and installed the head of Congress, Roberto Micheletti, as the interim president. Much of the international community, including the UN and the OAS, condemned it as a military coup.

Immediately following the coup, the Obama administration, including Secretary Clinton, publicly condemned the ouster of Zelaya. Over the following days, the U.S. position began to shift from demanding Zelaya's unconditional return to holding new elections.

Clinton helped organize elections where Zelaya and his supporters would be excluded. In her own words, she "strategized on a plan to restore order in Honduras and ensure that free and fair elections could be held quickly and legitimately, which would render the question of Zelaya moot".

Emails released later show that the 2009 removal was supported by Hillary Clinton's State Department by not recognizing it as coup in order to maintain U.S. aid to the Honduran people. Clinton and her team worked behind the scenes to stall military and economic efforts by Brazil, Argentina, Venezuela and Chile through the Organization of American States to restore Manuel Zelaya to office. "The OAS meeting today turned into a non-event — just as we hoped," wrote one senior State Department official, celebrating their success in defusing what they judged would have been a violent or destabilizing restoration.

The violence that followed the coup also led to a long-term increase in the country's murder rate, with a significant number of deaths occurring in the following years due to factors like political violence against activists and increased organized crime. Violence against LGBT people escalated significantly after the coup. Between 2009 and 2016, 229 LGBT people were murdered, a sharp increase compared to previous years.