Throughout the case, which involved a Trump real estate development on the West Side of Manhattan and a partnership with Hong Kong businessmen, Justice Lowe issued orders Mr. Trump’s lawyers said were biased.

By the end of the case, Mr. Trump’s top lawyer, Jay Goldberg, apologized for seeking to oust Justice Lowe from the proceedings, promising to never level such accusations against him again.

But when the litigation was going on, Mr. Goldberg forcefully challenged Justice Lowe’s “fitness to serve in a judicial capacity,” accused him of “unwarranted bias toward Trump” and said that, “at every turn, Justice Lowe has shown that he is unable to comply with his duties,” according to a 2009 complaint Mr. Goldberg submitted to the New York State Commission on Judicial Conduct.

Mr. Goldberg, a longtime lawyer for Mr. Trump, claimed that Justice Lowe had betrayed a bias against Mr. Trump on two occasions. The first, he said, was when Justice Lowe declared, in his chambers and in the presence of a lawyer for Mr. Trump, that he would not allow Mr. Trump’s presence in the courtroom to intimidate him. The second, Mr. Goldberg said, was when Justice Lowe allegedly told Representative Charles B. Rangel of New York that he did not like Mr. Trump.

Justice Lowe on Monday declined to comment on the case. During a 2009 hearing in which he denied Mr. Goldberg’s request for his recusal, he acknowledged that he had used the word “intimidate” in reference to Mr. Trump, saying he was generalizing that nobody could scare him. He also defended his rulings in the case and said any allegation that he had been unfair to Mr. Trump was “mind-boggling.” He questioned whether it was “an effort to change the course of this litigation by trying to get before another judge.”