A muted but defiant Mayor Eric Adams, in back-to-back appearances inside a federal courthouse in Manhattan and outside its granite facade on Friday, professed his innocence of criminal charges including bribery and fraud and stood by as his lawyer railed against the evidence in a case that threatens to topple his embattled administration.

“I am not guilty, your honor,” Mr. Adams said at his midday arraignment before Magistrate Judge Katharine Parker in a 26th-floor courtroom in Lower Manhattan, as reporters looked on from the gallery and via livestreams in several overflow courtrooms.

The indictment against Mr. Adams, a 57-page description by prosecutors of free, or heavily discounted, overseas trips and illegal campaign contributions from Turkey in return for political favors, has upended New York City’s political landscape. The will-he-or-won’t-he questions about whether Mr. Adams would resign seemed to overshadow even the upcoming presidential election as a tumultuous week in the city drew to a close.

Mr. Adams gave no sign that he was considering stepping down, and such an outcome seemed unlikely to happen at least before his next scheduled court appearance on Wednesday, when his lawyer has indicated he plans to attack the government’s case.

“This case isn’t even a real case,” the lawyer, Alex Spiro, said to reporters outside the courthouse. “This is the ‘airline upgrade corruption’ case.”

At around the same time, federal and state agents seized the phone of the mayor’s chief adviser and perhaps closest ally, Ingrid P. Lewis-Martin, a friend of the mayor’s for 40 years and his deputy when he was Brooklyn borough president. She was met at Kennedy Airport upon returning from a vacation in Japan, according to people with knowledge of the matter.