In the latest case against Mr. Temer, the lower house of Congress must once again vote on whether it should go to trial in the Supreme Court. While analysts believe that the president will avoid prosecution given Brazilians’ weariness of political upheaval, it is likely to come at a price and stand in the way of making headway on his reform agenda. He needs at least 172 of the 513 lawmakers to back him.

In June, Mr. Temer became Brazil’s first sitting president to face criminal charges when the attorney general charged him with accepting a $152,000 bribe. Last month, the lower house voted to spare Mr. Temer from standing trial in that case. In the weeks before the vote, Mr. Temer doled out millions of dollars in federal money to key congressional districts, in what some critics called an effort to sway lawmakers.

Mr. Temer has vehemently denied all allegations of wrongdoing and tried to have Mr. Janot removed from all cases related to him, arguing that the charges were politically motivated. This week, the Supreme Court denied the request.

Despite an approval rating in the single digits, Mr. Temer has rallied support among investors by portraying himself as the only leader capable of pulling Brazil out of the economic quagmire left by his predecessors from the leftist Workers’ Party. And while he has used up much of his political capital in Congress, a new twist in the investigation is expected to work in his favor.

Both the initial charges and this latest round are based on the testimony of top executives of the meat-processing giant JBS, Joesley Batista and his brother Wesley. As part of a plea bargain that enabled them to avoid prison, the brothers testified that Mr. Temer and several other politicians had accepted bribes.