It seemed an unusual choice when Fani T. Willis, the district attorney in Fulton County, Ga., turned to a suburban defense lawyer to oversee what seemed the biggest task of her career: building an election interference case against former President Donald J. Trump.

Nathan Wade, whom Ms. Willis tapped for the job, had little experience as a prosecutor. But he was a trusted friend and mentor, she said in 2022, willing to take the job when more seasoned prosecutors were not.

Now the relationship between Ms. Willis and Mr. Wade has taken center stage in the Georgia case against Mr. Trump, who is awaiting trial along with 14 co-defendants on charges of conspiring to overturn the former president’s 2020 election defeat in the state.

On Monday, a lawyer for one of the co-defendants, Michael A. Roman, charged in a court filing that Ms. Willis and Mr. Wade were romantic partners who were “profiting significantly from this prosecution at the expense of the taxpayers.” Without offering any proof, the filing accused the two of taking vacations together with money Mr. Wade had made while working for Ms. Willis’s office as a special prosecutor. In all, the office has paid Mr. Wade $653,881, according to county records.

Neither Ms. Willis nor Mr. Wade has commented publicly on the allegations. A spokesman for Ms. Willis said on Monday that her office would “respond appropriately in court.”

Mr. Roman’s defense lawyer, Ashleigh B. Merchant, argued that it all amounted to a conflict of interest that should disqualify Mr. Wade, Ms. Willis and the entire Fulton County district attorney’s office from prosecuting the case.

“As the layers unfold,” Ms. Merchant wrote in her filing, “it becomes clear that the district attorney and the special prosecutor have been profiting personally from this prosecution at Fulton County’s expense.”

Whether the filing has the power to knock the case off the rails remains to be seen, although a number of legal experts said this week that some of Ms. Merchant’s efforts to have the case dismissed were unlikely to succeed.

But the matter has already become an embarrassing one for Ms. Willis, placing the case under a cloud of suspicion and bolstering Mr. Trump’s longtime efforts to delegitimize the case and paint Ms. Willis as corrupt.

According to a court filing obtained by The New York Times, Ms. Willis was served on Monday with a subpoena in Mr. Wade’s ongoing divorce case from his wife, Joycelyn Wade. In the document, a process server affirms that he left the subpoena with an assistant to Ms. Willis at her downtown Atlanta office.

Andrea Hastings, a lawyer for Ms. Wade, said she had sent the subpoena requesting that Ms. Willis testify at a deposition on Jan. 23. News of the subpoena was reported earlier by The Wall Street Journal.

In arguing for the case to be dismissed, Mr. Roman’s legal team wrote that Ms. Willis had failed to properly obtain the approval of the Fulton County commission before hiring Mr. Wade. But on Tuesday, Pete Skandalakis, a Republican who leads the Prosecuting Attorneys Council of Georgia — a state agency that provides services to prosecutors — said that district attorneys in Georgia were not required to seek the authorization of county commissions before making such hires.

Ms. Merchant also argues that the district attorney’s office did not properly file Mr. Wade’s oath of office. But a similar argument made by another co-defendant in the case has already been rejected by the presiding judge.

Also unclear is whether proof will emerge of a romantic relationship between the two prosecutors. Ms. Merchant said on Monday night that she believed Mr. Wade’s sealed divorce proceedings contained proof that the pair had traveled together; she is trying to make the divorce file public.

But the allegations have already been seized upon by Mr. Trump, who in August made an unsubstantiated claim that Ms. Willis was having an affair with a gang member, which she strongly denied. On Tuesday evening, he sent a fund-raising email to supporters saying that the case “must be THROWN OUT!” and saying that Ms. Willis had “reportedly used the phony case against me to hire her ‘lover’ in a SELF-ENRICHMENT SCHEME of more than half a MILLION dollars!”

A number of experts in law and ethics who reviewed the new motion were skeptical that it would blow up the case, although some said that issues that it raised warranted further investigation and could harm the public’s trust in the prosecution.

Renee Knake Jefferson, an ethics expert and a law professor at the University of Houston Law Center, said she thought that the filing included serious allegations but that they were not likely to tarnish the indictment.

“A personal relationship between two prosecutors does not change the facts and evidence upon which the indictment was based,” Ms. Jefferson said.

Ms. Jefferson said it was important to get to the bottom of the nature of the relationship between Ms. Willis and Mr. Wade to determine whether either or both should be removed from the case.

Ms. Willis has hired a number of outside lawyers to help her with the sprawling Trump case, which centers on a complex racketeering indictment that initially listed 19 co-defendants. Four have pleaded guilty since the indictment was handed up in August.

In addition to Mr. Wade, the outside lawyers include John Floyd, a mild-mannered, binder-toting man with deep expertise in racketeering laws, and Anna Cross, an experienced trial lawyer who subjected Mark Meadows, Mr. Trump’s former White House chief of staff and a defendant in the case, to a withering cross-examination in a related federal court hearing in September.

In her 2022 interview, Ms. Willis said that she had chosen Mr. Wade for the job because he was a trustworthy friend and contemporary (she is 53, Mr. Wade 54) whom she thought thick-skinned enough to handle not only attacks from Trumpland but her own critiques.

“Sometimes this new generation, you can’t yell at them, and they’re kind of weak, right?” Ms. Willis said, adding, “I need somebody I can go off on, and they can, like, wipe off their wounds and we can get back to work.”

Still, the appointment of Mr. Wade to head up the criminal prosecution of a former president raised some eyebrows in Atlanta’s legal community given his limited work trying serious criminal cases. His only known full-time work as a prosecutor was as an assistant solicitor in Cobb County, in the Atlanta suburbs, between October 1998 and May 1999, according to Ross Cavitt, a county spokesman. That job typically involves handling misdemeanor cases.

(Mr. Wade advertises that he was appointed a “special assistant attorney general” for the state, but Kara Richardson, a spokeswoman for the attorney general’s office, said in August that she could find no record of cases he worked on for that office.)

Mr. Wade, who could not be reached for this article, earned a law degree from the John Marshall Law School in Illinois, which was eventually merged with the law school at the University of Illinois at Chicago. In hearings related to the Trump case, he projects confidence, typically striding into courtrooms in well-tailored suits, surrounded by a gaggle of fellow prosecutors.

Though he speaks occasionally with the presiding judge, he also seems comfortable letting various team members take the limelight during oral argument.

In private practice, he appears to have been a legal jack-of-all-trades. The website of his law firm, Wade & Campbell, declares: “Whether you are in need of representation after a major car accident or are going through a change in your personal life that requires representation with a family law issue; whether you have a contract dispute, or whether you are involved in any type of civil litigation, Nathan J. Wade will be a zealous advocate for you.”

In the future, Mr. Wade may be able to add language about prosecuting a former president to that list — but only if he survives the current storm.