Nearly three years after she began investigating former President Donald J. Trump and his allies, Fani T. Willis is facing the biggest test of her handling of the landmark election interference case.

Ms. Willis, the district attorney of Fulton County, Ga., was accused this week of being romantically involved with the lead prosecutor she hired for the Trump case, a turn of events that has invigorated Republicans and raised a flurry of questions about her conduct and judgment. The prosecutor, Nathan Wade, has reaped more than $650,000 in legal fees.

While many legal experts doubt that the accusations — if true — will derail the case, they could present significant problems for Ms. Willis and create distractions around the case. The allegations have already created a firestorm on the political right, with Mr. Trump and his allies accusing her of violating a raft of county and state laws. They have even given pause to some Democrats.

“If the allegations are true — and it’s a big if — it’s troubling,” Robb Pitts, a Democrat who is chair of the Fulton County Board of Commissioners, said in an interview this week. “To have this come up at this point in time, and at this point in this trial, can raise questions.”