Gen Gilbert Diendere, the head of Blaise Comapore’s presidential guard, was detained for seizing power in September 2015.
He has been charged with 11 crimes including threatening state security, murder, collusion with foreign forces, voluntary assault and wilful destruction of property.
Blaise Compaore, no relation to the interior minister, is exiled in neighbouring Ivory Coast.
He was driven out of power by crowds opposed to his bid to change the constitution to extend his 27-year rule.
He was accused of committing widespread abuses during his rule.