The City Prosecutor's Office represents the City in prosecuting violations of City ordinances in Municipal Court. Municipal Court is located in the basement of the Buchanan County Courthouse at 411 Jules Street and is presided over by the Municipal Judge, who is elected during the general municipal election, which occurs every four years.

Complaints that involve incidents that occurred in Buchanan County (but occurred outside the St. Joseph City limits), violations of State law, and all felony charges are referred to the Buchanan County Prosecuting Attorney.