Prosecutor Pablo Turano want to investigate Messi, his father Jorge, and anyone involved in the running of the organisation in relation to allegations of money laundering.
'La Nacion' report that the complaint is in relation to donations recieved by the organisation in Argentina.
An ex-employee of the Messi Foundation seems to have been key in Turano building his case, revealing supposed illegalities with how the money was handled.
A member of the Messi team affirmed in 'Clarin' that the "complaint is baseless".
A judge will now have to decide if there is enough evidence to open a case against the organisation.