The attorney had represented Eric Trump since the case was filed in August 2020, and Mr Trump will continue to be represented by criminal defence attorney Alan Futerfas.
Mr Mukasey is a former law partner of Rudy Giuliani and represented Navy SEAL Eddie Gallagher who was accused of killing dozens of Iraqi civilians during his deployment.
He was court-martialed in 2019 and found not guilty of first-degree murder and attempted murder.
But he was found guilty of posing with the body of a 17-year-old ISIS fighter in Mosul, Iraq, in 2017.
The one-term president then pardoned Gallagher and ensured that no disciplinary action would be taken against him by the Navy.
Mr Mukasey has also represented basketball coach Rick Pitino in criminal investigations, and oil-field service company Halliburton.
The Trump Organization is being investigated by New York attorney general Letitia James over allegations it falsified the value of its assets to secure loans and tax breaks.
The Independent has reached out to Mr Mukasey for comment.
Mr Trump went on Fox News recently to complain about the barrage of subpoenas the Trump Organization and members of the Trump family have received.
On Sunday, Mr Trump told Fox News host Maria Bartiromo that the Trump team is facing several investigations and that they have to respond to subpoenas “every single day”.
“The problem with the Democrats is they dig so deep that they always find themselves,” Mr Trump said.
“And the reason I’m frustrated about this is every single day since my father ran for president, my father and our entire family and our company has been under investigation. Every single day, Maria, we get subpoena after subpoena after subpoena.”
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