Mr Trump received an additional charge of wilful retention of defence information, and two new charges of obstruction, the justice department said.
An additional person, Mar-a-Lago staff member Carlos de Oliveira, has also been indicted in the case.
Mr Trump has pleaded not guilty.
Mr Trump's aide Walt Nauta - who has similarly entered a not guilty plea - also received two additional counts of obstruction.
The new court documents outline alleged efforts between Mr Nauta and Mr de Oliviera, the property manager at Mar-a-Lago, to obstruct the justice department's investigation.
According to the new court documents, Mr Nauta and Mr de Oliveira conspired to delete footage from security cameras after the Department of Justice issued a subpoena asking for surveillance footage of the basement where it said confidential documents were held.
In the court documents, Mr de Oliveira is claimed to have texted another employee who was the director of information technology that "the boss" wanted the server deleted.
The documents allege that Mr de Oliveira later met with the employee in a small room, told him them their conversation should remain private, then pressured the man into obliging his request after the employee told Mr de Oliveira that he did not have the authority.
"What are we going to do," Mr de Oliveira allegedly asked his co-worker. A lawyer for Mr de Oliveira has declined to comment.