The 51-year-old was apprehended in the couple's home in the east of the capital Tegucigalpa, a spokesman for the country's supreme court, Melvin Duarte, told AFP.
She was implicated in an investigation showing the equivalent of USD 500,000 had allegedly been siphoned off into her personal account six days before her husband stepped down as president on January 27, 2014, Duarte said.
Ana Maria Calderon, head of MACCIH, an anti-graft body in the country set up under the Organization of American States, told a news conference the former first lady's office was suspected of embezzling a total USD 4 million between 2011 and 2014.
She added that at least nine employees working for Bonilla were thought to have been involved in the alleged plunder. The charges were for embezzlement of public funds, money laundering, and criminal association.
According to the National Anti-corruption Council, Bonilla's official bank account also received USD 638,000 from a state agency for children.
Duarte said Bonilla would be brought before a criminal court judge handling corruption cases who would decide whether to jail her or not.
MACCIH was created in February 2016 at the request of current President Juan Orlando Hernandez after a wave of protests against the transfer of more than USD 330 million out of the country's social security coffers.
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