Otto Perez Molina and Roxana Baldetti are among 70 people accused of involvement in a scheme that embezzled millions of dollars of government money.
Both strongly deny the accusations.
Mr Perez Molina, who was elected in 2012, and Ms Baldetti are already facing trial in another case that led to their resignations last year.
Announcing the latest charges, Prosecutor Julio Barrios Prado said the pair had been involved in illegal financing, embezzlement and money laundering.
Addressing Mr Perez Molina in court he said: "That money was used to buy goods and services for you and Baldetti including real estate and luxury vehicles, as well as $4.3m (Â£3m) in gifts."
He said shell companies had been used to try to conceal the money.
Ms Baldetti is also accused of receiving $38m (Â£26.6m) in bribes for government contracts. Prosecutors allege that, on one shopping trip to Miami, she spent more than $27,000 of the cash on shoes and clothing.
Mr Perez Molina and Ms Baldetti are already facing trial over a corruption scheme dubbed La Linea (The Line) that involved businesses paying bribes to government officials and custom officers in return for being allowed to evade import duties. They have denied any wrongdoing.
A former president and vice-president of Guatemala have been formally charged with corruption and money-laundering.