Spanish football giants Real Madrid and Barcelona are among seven teams under investigation over allegations of irregular public funding.
The European Commission is looking into whether four teams have benefited from unfair tax advantages.
Real Madrid, Barcelona, Athletic Bilbao and Osasuna – who are exempt from having to convert to sport limited companies – pay corporation tax at a 25% rate.
Limited sport companies pay the tax at a 30% rate.
In a separate probe the commission will look into the sale of Real Madrid’s training ground. It was valued at €22.7 million as part of a land swap with the City of Madrid. Its value in 1998 was around 600,000 euros.
The commission will also investigate Valencia, Hercules and Elche, who are alleged to have received state-backed loans up to €75m.
European Competition Commissioner Joaquin Almunia announced the investigation at a news conference in Brussels.
But the fact that Almunia is a Bilbao fan and was a minister in the Spanish government that signed off on the tax rules could imply a conflict of interest, said ombudsman Emily O’Reilly, whose job is to address complaints about maladministration in EU bodies.