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Paul J. Manafort, President Trump’s former campaign chairman, pleaded not guilty on Thursday to mortgage fraud and other charges brought by the Manhattan district attorney in an effort to ensure Mr. Manafort could still face prison time if he is pardoned for his federal crimes.

The state charges against Mr. Manafort include allegations that he falsified business records and engaged in a conspiracy to obtain millions of dollars in loans for several New York homes.

Mr. Manafort’s lawyer has contended that the state indictment should be dismissed because his client has already been tried in federal court on charges based on some of the same conduct, and he should not be prosecuted a second time.

Appearing in New York State Supreme Court before Justice Maxwell Wiley, Mr. Manafort wore navy blue scrubs and white sneakers, his hands shackled at his waist. He walked with a slight limp and had to be helped into a seat.

“Not guilty,” he said when asked how he pleaded to the charges.

Outside the courthouse, Mr. Manafort’s lawyer, Todd Blanche, said he was filing a motion to dismiss the case on the grounds the indictment violated state law regarding double jeopardy. “In our view, the laws in New York do not allow the people to do what they did in this case,” he said.

Mr. Manafort has been serving a seven-and-a-half year sentence at a federal prison in Pennsylvania after being convicted of tax and bank fraud in two federal cases. Those cases were brought by the special counsel, Robert S. Mueller III, during his investigation into Russian interference in the 2016 election.

Mr. Manafort, who worked for Mr. Trump’s 2016 presidential campaign, was brought to New York a week ago to face the state charges, which were filed in March.

Normally, inmates awaiting court appearances on state charges would be held in the notorious Rikers Island jail complex. But Mr. Manafort was permitted to be held in the Manhattan Correctional Center, a federal prison, after the second-highest law enforcement official in the country intervened.

Beyond the mortgage fraud case against Mr. Manafort, state authorities in New York also are pursuing several investigations focused on Mr. Trump, his associates and his business. These include civil inquiries into the Trump Organization’s insurance practices, real estate deals and the family’s charitable foundation.

Mr. Trump has not said he intends to pardon his former campaign chairman, but he has often spoken of his power to do so and he has defended Mr. Manafort on a number of occasions, calling him a “brave man.” The president has broad power to issue pardons for federal crimes, but he has no such authority in state cases.

The state charges against Mr. Manafort grew out of an investigation that began in 2017, when the office of the Manhattan district attorney, Cyrus R. Vance Jr., began examining loans Mr. Manafort received from two banks.

The 16-count indictment unveiled in March said the fraud occurred between December 2015 and January 2017, but contained few details.

Several people with knowledge of the matter said the mortgage fraud charges stemmed from loans Mr. Manafort obtained or tried to obtain from Citizens Bank, based in Rhode Island, and Federal Savings Bank in Chicago.

The loans were for properties on Howard Street in Lower Manhattan; on Union Street in Brooklyn Heights; and in Bridgehampton on Long Island, the people said.

Mr. Manafort could face up to 25 years in New York State prison if convicted of the most serious charges in the indictment.

Just before the state charges were announced, Mr. Manafort, 70, was sentenced in Virginia to nearly four years in prison on one of his two federal convictions. He was then sentenced in Washington, D.C., to serve an additional three and a half years on the other case.

The financial fraud charges at the heart of Mr. Vance’s case were the basis for some of the counts in the federal indictment in Virginia. Manhattan prosecutors had deferred their inquiry to avoid interfering with Mr. Mueller’s broader investigation into Russian meddling in the 2016 presidential election.

“No one is beyond the law in New York,” said Mr. Vance in announcing the charges against Mr. Manafort on March 13.

In the Virginia trial, Mr. Mueller’s prosecutors presented evidence that Mr. Manafort lied to obtain bank loans, evaded taxes and used foreign accounts to hide millions of dollars earned from his political consulting work in Ukraine. A month later, he pleaded guilty in the related federal case in Washington, D.C.

The convictions marked the end of a swift fall for Mr. Manafort, who once moved in elite circles and commanded large fees as a political consultant. He wore luxurious clothes, including a $33,000 blue lizard jacket and $12,000 suits.

As part of a plea deal with federal prosecutors, Mr. Manafort forfeited five homes in New York, worth about $22 million, to the government.

The Fifth Amendment of the United States Constitution protects Americans from being tried twice for the same crime, a condition known as double jeopardy.

Mr. Vance’s office is expected to argue that an exception is warranted in Manafort’s case, and prosecutors in Mr. Vance’s office have expressed confidence that they will prevail, according to people with knowledge of the matter.

Victoria Bekiempis and William K. Rashbaum contributed reporting.

Sharon Otterman has been a reporter at The Times since 2008, primarily covering education and religion for Metro. She won a Polk Award for Justice Reporting in 2013 for her role in exposing a pattern of wrongful convictions in Brooklyn. @sharonNYT

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