Prosecutor General Paulo Gonet charged Bolsonaro and his running mate, General Walter Braga Netto, with leading a "criminal organisation" that aimed to overthrow Brazil's 40-year-old democracy.
A total of 34 people were charged in the plot, including several military officials, such as Bolsonaro's former national security adviser, retired General Augusto Heleno, and former Navy Commander Almir Garnier Santos, according to the charge sheet.
"The responsibility for acts harmful to the democratic order falls upon a criminal organisation led by Jair Messias Bolsonaro, based on an authoritarian project of power," it added.
Analysts consider it unlikely Bolsonaro will be arrested before his trial, unless Supreme Court Justice Alexandre de Moraes, who is overseeing the case, deems him a flight risk.
The case echoes the criminal charges faced by US President Donald Trump that accused him of seeking to overturn his own re-election loss in 2020. That case was repeatedly delayed and ultimately dropped after Trump was returned to power in last November's US election.
The charges against Bolsonaro come just months after Brazil's federal police concluded a two-year investigation into his role in the election-denying movement that culminated in the riots by his supporters that swept the capital, Brasilia, in early 2023, a week after President Luiz Inacio Lula da Silva took office.
At the time, many protesters admitted that they wanted to create chaos to justify a military coup that they considered imminent. Late last year, police arrested five alleged conspirators suspected of planning to assassinate the leftist Lula before he took office.
Prosecutors have said the Bolsonaro-led plot included plans to poison Lula, a one-time union leader who previously served two terms as president.
Lula narrowly defeated the right-wing standard-bearer in the late 2022 presidential election.
"They sought total control over the three branches of government; they outlined a central office that would serve the purpose of organising the new order they intended to establish," the charging document noted, referring to those who allegedly pushed the coup plot.
Bolsonaro, a former army captain, has repeatedly denied breaking any laws, and calls allegations against him a witch hunt by his political opponents.
Lawyers representing Bolsonaro said in a statement that he never supported any movement aimed at dismantling Brazil's democratic rule of law or the institutions that uphold it.
Meanwhile, Senator Flavio Bolsonaro, a son of the former president, in a post on X on Tuesday night derided the charges as an "unconstitutional and immoral mission to attend to Alexandre de Moraes' whims and Lula's nefarious interest."
The indictment marks the first time Bolsonaro has been charged with a crime, though he has faced several legal challenges to his conduct as president since he lost his re-election bid.
Two previous decisions by Brazil's Federal Electoral Court have already blocked him from running for president until 2030.
Bolsonaro's lawyers have two weeks to respond to the charges before the Supreme Court decides whether it will accept the charges and potentially hold a dramatic, televised trial.
If convicted, Bolsonaro faces at least a dozen years behind bars.
with Reuters
