Walt Nauta was charged alongside Mr Trump in June in a 38-count indictment alleging the mishandling of classified documents.
Mr Trump also pleaded not guilty during his June 13 arraignment to charges including wilful retention of national defence information.
But Mr Nauta's arraignment was postponed that day because of his inability to retain a lawyer licensed in Florida and then was pushed back again last week when a flight from New Jersey he was to have taken was cancelled, AFP reported.
The indictment filed by special counsel Jack Smith and his team of prosecutors accuses Mr Nauta of conspiring with Mr Trump to conceal records that the former president had taken with him from the White House after his term ended in January 2021.
Mr Nauta faces six counts of conspiracy to obstruct justice, false statements, and withholding and concealing documents.
Prosecutors allege that Mr Nauta, at the former president’s direction, moved boxes of documents bearing classification markings so they would not be found by a Trump lawyer who was responsible for searching the home for classified records to be returned to the government.
That, prosecutors said, resulted in a false claim to the Justice Department that a “diligent search” for classified documents had been done and that all documents responsive to a subpoena had been returned.
Mr Nauta is a US Navy veteran who worked for Mr Trump as his valet at the White House before joining him as a personal aide at Mar-a-Lago.
He can regularly be seen by Mr Trump’s side, including travelling in his motorcade to the Miami courthouse for their appearance earlier this month.
Despite the many charges facing him, Mr Trump is the front-runner for the 2024 Republican presidential nomination.
Mr Trump is the first US president past or present to face criminal charges in both federal and state courts.
In addition to the documents case, Mr Trump was charged in New York with allegedly falsifying business records to cover up hush money payments to an adult film star during his 2016 presidential campaign.
The former president has denied any wrongdoing and says the investigations are part of a political plot against him.
The judge in the case has set a July 14 hearing over how classified information in the case will be handled.
Legal experts have said the complexities surrounding the use of highly classified documents as evidence are likely to delay Mr Trump's trial.