Gen Gilbert Diendere is expected to face trial before a military tribunal.
Interim President Michel Kafando was reinstated two weeks ago after intervention from the army and West African leaders.
The presidential guards’ unit that carried out the coup is to be disbanded.
BBC West Africa correspondent Thomas Fessy says Gen Diendere has been formally charged with 11 crimes including threatening state security, murder, collusion with foreign forces, voluntary assault and wilful destruction of property.
Former Foreign Minister Djibril Bassole, who was also arrested in connection with the coup, has also been charged. Mr Bassole has always denied any involvement.
Last week, Gen Diendere was reported to have surrendered to the authorities in the capital Ouagadougou.
Some of his forces had refused an order to disarm, forcing the army to attack their base in the city.
The elite Presidential Security Regiment (RSP) is loyal to Blaise Compaore, the country’s long-time ruler who was ousted in a popular uprising last year.
Unhappy about being integrated into the regular army, members of the unit stormed the cabinet room on 16 September, seizing Mr Kafando, the prime minister and others.
A week later, when it became clear they did not enjoy popular support and after an ultimatum from the regular army, the RSP withdrew from the capital.
The regional bloc Ecowas also helped to bring an end to the crisis.
At least 10 people were killed and more than 100 injured in clashes during the takeover, which Gen Diendere later described as “the biggest mistake”.
Burkina Faso is due to hold general and presidential elections on Sunday.