Hoeness made a self-denunciation about unpaid taxes on funds he held in a Swiss bank account earlier this year.
In reporting himself to the tax authorities, and voluntarily paying an undisclosed amount to cover the shortfall, Hoeness was hoping to avoid any further sanctions.
However, after examining Hoeness' accounts and his self-denunciation, Munich's state prosecutors filed charges against him on Tuesday.
"The Munich state prosecutors II concluded their investigations into the case of Ulrich. H (Hoeness) on 29.07.2013 and pressed charges to the fifth criminal chamber of the Munich regional court II,'' read a statement from the Munich state prosecutors.
"The accusation, in which the 61-year-old president of FC Bayern Munich is being accused of tax evasion, has now been submitted.''
The Munich regional court must now decide whether to open a trial against the president of the European and German champions, based on the evidence provided by the state prosecutors.