Bongo and his main rival Albert Ondo Ossa lead a race of 14 candidates vying for the top job in the small oil-rich central African state.
Even before voting stations opened at 0600 GMT, a handful of people were waiting to cast their ballots at five schools in the centre of Libreville — though most of the streets, decked out in the colours of Bongo's governing party, were still empty, an AFP journalist saw.
The 64-year-old incumbent took office in 2009, succeeding his father Omar, who died after more than 41 years in power.
But shortly ahead of the elections, a storm erupted over a purported conversation between Ondo Ossa and a fellow opposition figure.
The conversation — recorded without the pair's knowledge and disseminated on social media — refers to various strategies "to create a power struggle" and support from other countries.
Bongo has accused the pair of treason, saying the remarks reflect a plot to take over with the help of "foreign powers."
At an eve-of-election rally attended by tens of thousands of supporters in Libreville, Bongo charged that the two sought to "destroy this country."
"We won't let them to do it," he said.
Onda Ossa, a 69-year-old economics professor who served as a minister under Bongo from 2006 to 2009, was chosen by the main opposition grouping, Alternance 2023, as its joint candidate just eight days before the election.
Alternance 2023 this week issued a statement strongly denying the "veracity and authenticity of this conversation" and accused the government of "shameful manipulation."