The Pontotoc County grand jury handed down the four count indictment against Laura L. Franklin, 64, of Pontotoc.
Franklin is accused of taking money and other property for her own use from the church.
She is also accused of issuing a check for more $500 for her own use and using the church's credit cards to buy Ole Miss football tickets.
Court documents say the total amount in dispute is $537,277.74.
Franklin entered the not guilty plea during a hearing in Lee County Circuit Court.
She is currently free on a $25,000 bond.