The Ombudsman was asked to look into the Commission's handling of three cases of state aid and a request for information and access to documents, it said.
The complainant, a shareholder in an unidentified Spanish football club, had given information to the Commission in 2011 and 2012 about what he believed were three cases of illegal state aid given to football clubs.
The first involved alleged non-payment of taxes and social security contributions by all football clubs in Spain. The second case involved real estate transactions between a club and a local body, and the third concerned a bank loan given by a publicly-owned bank to a club.
One year after making the allegations the complainant asked the Ombudsman to look into the handling of the investigations, saying that the Commission had taken too long to decide whether to open a formal investigation. Because of this delay, the complainant had also asked for access to some documents relating to two of the cases, but was refused.
The Ombudsman ruled that there had been no maladministration by the Commission on either issue, and that officials were justified in refusing access to the documents.
Competition law expert Angelique Bret of Pinsent Masons, the law firm behind Out-Law.com said: "This decision serves as a reminder of the fact-specific nature of state aid investigations, the considerable discretion that the Commission enjoys in managing investigations, and the relatively high bar for securing interested party status."
"This is not the first time in recent history that the Commission has been accused of mishandling competition investigations in relation to issues affecting Spanish football clubs. In May 2013, football agent Daniele Striani complained to the Commission, alleging that the Union of European Football Associations (UEFA)'s financial fair play rules infringed European Union Treaty rules on antitrust. The Commission refused to investigate it on priority grounds," Bret said.
"In December 2014, Striani complained to the European Ombudsman, alleging that the refusal of the complaint had been motivated by conflicts of interest. Striani said that the decision of the then-competition commissioner Joaquín Almúnia, a Spaniard, had been coloured by improper ties with an affected Spanish club and with the UEFA president at the time, Michel Platini. The European Ombudsman rejected this complaint, pointing to the fact that investigations into alleged illegal state aid to Spanish football clubs had been opened during Almúnia's tenure. One of those state aid investigations was the subject of yesterday's decision," she said.