The objections the EU was looking into centered on how Spanish clubs and local authorities handled fiscal issues such as loan guarantees, land swaps or construction funding.
The EU ombudsman's services said a complainant in the case said the state aid totals several billion euros, adding that the Commissioner had been considering the issue for years before announcing Wednesday's opening of proceedings.
More importantly, Almunia also said he might look beyond the specific case raised Wednesday.
"I have also read about the questions on the high debts of the (soccer) football clubs to the economics ministry," Almunia said.
In April, Spain's Sports Council said Spanish soccer clubs owed the government 670 million euros ($874 million) in taxes.