Former President Donald J. Trump and an employee, Walt Nauta, pleaded not guilty on Thursday to additional criminal charges in the case accusing the former president of illegally holding onto secret national security documents after leaving office and conspiring to obstruct the government’s efforts to retrieve them.

The plea to the added charges was entered for Mr. Trump by one of his lawyers after an updated indictment last month that accused him of seeking to delete security footage at his Mar-a-Lago residence and club. Mr. Trump, who was first charged and arraigned in person in June, chose not to appear at the federal courthouse in Fort Pierce, Fla.

Last week, he signed a form forgoing his appearance and indicating that he would plead not guilty. During a 10-minute hearing Thursday, Todd Blanche, a lawyer for Mr. Trump, told a magistrate judge that he had discussed the expanded charges with his client, who “has authorized me to enter a plea of not guilty.”

Two employees of Mr. Trump whom prosecutors also accused of conspiring to delete the footage, Mr. Nauta and Carlos De Oliveira, were also charged in the revised indictment and appeared at the hearing.

Mr. Nauta stood next to his lawyer, Stanley Woodward Jr., his hands clasped as Mr. Woodward entered a not guilty plea on his behalf.

While Mr. De Oliveira also attended the hearing, his lawyer, John Irving, said that they were still trying to find a local lawyer, which he is required to have before he can be arraigned. Donnie Murrell, a lawyer based in West Palm Beach, stood with them and told the judge that he thought they could strike a deal by Friday.

The magistrate judge, Shaniek Mills Maynard, rejected a suggestion that Mr. De Oliveira’s arraignment be delayed until Aug. 25, when a hearing in the case has been scheduled, scheduling it instead for 10 a.m. on Tuesday. But Mr. De Oliveira did not need to attend, she said.

The updated indictment also added a count against Mr. Trump under the Espionage Act related to a national security document that he is accused of showing to visitors at his golf club in Bedminster, N.J.

Prosecutors say Mr. Trump showed off the document, a battle plan related to attacking Iran, during a meeting at his Bedminster golf club, to two people helping his former White House chief of staff Mark Meadows write a book. In an audio recording of that meeting, Mr. Trump can be heard rustling paper, and saying “as president I could have declassified it” but it was “still secret.”

The updated indictment says that document was found among 15 boxes of files that Mr. Trump returned to the National Archives and Records Administration in January 2022, months after the agency had sought to get them back.

Mr. Trump has claimed that he never had the Iran battle plan at that meeting and was referring to something else in the recorded conversation.

Around the time that the hearing began, Mr. Trump was in New Jersey, in a sand trap on the fifth hole at his Bedminster golf course.

The revised indictment also added obstruction allegations against Mr. Trump, Mr. Nauta, and Mr. De Oliveira. It accused them of conspiring to delete security camera footage from Mar-a-Lago after the government had sought to obtain it with a subpoena.

Mr. De Oliveira was also charged with one count of making a false statement to investigators, to which he also pleaded not guilty.

The trial will be overseen by Judge Aileen M. Cannon, not Judge Maynard, so the arraignment left unaddressed several early pretrial disputes under consideration by Judge Cannon.

A point of contention is over what limits should be imposed on Mr. Trump and his lawyers in handling and discussing classified evidence, a necessary first step in turning such material over to them to determine what can be used in the trial and how.

Prosecutors have also asked whether Mr. Woodward, who has represented many other people in Mr. Trump’s orbit, has a conflict of interest in representing Mr. Nauta because he has worked for at least three witnesses in the inquiry who could be called to testify.

In an order this week, Judge Cannon also asked both sides to “address the legal propriety” of Mr. Smith’s continued use of a grand jury in the District of Columbia even though that activity relates to the indictment brought in the Southern District of Florida.

The second arraignment in the documents case came a week after Mr. Trump appeared at a federal courthouse in Washington to plead not guilty to charges of conspiring to subvert American democracy in his efforts to stay in power despite losing the 2020 election.

He is also facing felony bookkeeping fraud charges in state court in New York, in connection with allegations that he caused his company to falsify business records to cover up a hush money payment during the 2016 campaign.

And in Georgia, a district attorney, Fani T. Willis, has suggested that Mr. Trump and several of his allies may soon be indicted over their efforts to subvert President Biden’s narrow victory over Mr. Trump in her state in 2020.

Alan Blinder contributed reporting from Bedminster, N.J.