Southaven Mayor Greg Davis faces one count each of embezzlement, false pretense and making fraudulent statements.
Davis has been under scrutiny since November 2011, when the Mississippi Auditor's office told him to repay $170,000 for improper billings, including travel, stress counseling and food and liquor. The amount was later reduced to $158,000.
The charges in the indictment were related to a city car, gasoline purchases and a $1,000 check.
The auditor's office has said that its investigation uncovered a wide range of questionable spending, including an alleged purchase at a gay sex shop in Canada.
After those allegations came to light, Davis announced that he is gay and said he and his wife had divorced. Some of the money Davis was ordered to repay as part of the auditor's investigation went to counseling for his family.
Davis, a Republican, is in his fourth term as mayor of Southaven, a suburb of Memphis, Tenn., that has grown rapidly in recent years to become Mississippi's third-largest city, after Jackson and Gulfport.
He has refused to resign as mayor despite calls from city officials and others for him to step down.
Davis served in the state House before he was elected mayor and ran unsuccessfully for north Mississippi's 1st District congressional seat in 2008. As a legislator and a congressional candidate, he talked frequently about being a fiscal conservative.