President Trump’s former campaign chairman Paul Manafort limped into Manhattan court Thursday to plead not guilty to mortgage fraud charges — but he still doesn’t know where he’ll be cooling his heels as the case winds through court.

Manafort, 70, is facing a 16-count indictment filed by state prosecutors and accusing him of lying in paperwork to obtain millions of dollars in loans for his various properties in New York.

“The grand jury of the County of New York … charges you with three counts of residential  mortgage fraud in the first degree and other related charges. How do you plead?” a Manhattan Supreme Court clerk asked him.

“Not guilty,” Manafort responded in a raspy voice while seated at the table in handcuffs.

The once dapper former Republican consultant — whose federal trial once centered on his $15,000 custom ostrich bomber jacket — looked disheveled in navy blue prison duds and white sneakers during his court appearance. He had a pronounced limp as he walked in and out the courtroom and sported grayer-than-usual hair.

Manafort is charged with residential mortgage fraud, attempted residential mortgage fraud, conspiracy, falsifying business records and scheme to defraud for allegedly providing bogus information in applying for residential mortgage loans from 2015 until 2017.

The longtime political operative is currently serving a 7½-year sentence stemming from two federal cases. He was convicted last year of misleading the US government about his lucrative foreign lobbying work, hiding millions of dollars from the IRS and encouraging witnesses to lie on his behalf.

The charges arose from special counsel Robert Mueller’s investigation into Russian meddling in the 2016 election.

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Manafort has been in custody at Federal Correctional Institute Loretto, a low-security lockup in Pennsylvania, but was transferred to the Metropolitan Correctional Center in Lower Manhattan — where notorious Mexican drug lord Joaquin “El Chapo” Guzman also is housed.

The Department of Justice said he will be kept in federal custody as his state case plays out — though it’s not yet clear exactly where.

Manafort’s lawyer, Todd Blanche, wants him sent back at Loretto, noting their health care and convenience for Manafort’s family to visit. But ultimately, it’s up to the Federal Bureau of Prisons to decide.

“He’s going to be held in federal custody, that’s all that was disclosed,” Blanche told The Post.

At the MCC, Manafort is being housed with other inmates, Blanche said.

The Manhattan District Attorney’s Office declined to comment on Manafort’s prison fiasco but in a filing indicated prosecutors may want to introduce as part of their case admissions Manafort made when he took a plea deal Sept. 14, 2018, in federal court in Washington, DC.

“Mr. Manafort admitted, orally, and in writing, to making misrepresentations in mortgage applications for properties located in New York, Kings, and Suffolk counties to two financial institutions,” according to the filing. “Additionally, Mr. Manafort admitted to making misrepresentations to another financial institution in a loan application.”

If convicted, the New York charges could keep him behind bars effectively for the rest of his life — even if he is pardoned by Trump. The president can only pardon people for federal crimes, not state offenses.

DA Cyrus Vance announced the charges against Manafort just minutes after he was sentenced in the second of his two federal cases.

“No one is above the law in New York,” Vance said at the time.

Blanche plans to fight the charges on the grounds of double jeopardy.

“We intend to move to dismiss the indictment based upon New York double jeopardy,” Blanche told reporters after the arraignment. “In our view, the laws of New York do not allow the People to do what they did in this case.”

But Manhattan prosecutors insist their case is rock solid — because mortgage fraud and falsifying business records are state crimes, but not federal crimes.

Manafort is due back in court Oct. 9, but Blanche asked that his future court appearances be waived. Judge Maxwell Wiley said he would consider that on a case-by-case basis.

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