In 2006, during the Operación Puerto doping case by the Spanish police, he was identified as the client of a doping traffic network led by Eufemiano Fuentes, under the code name Bonilla Alfredo.

[3] Bonilla was not sanctioned by the Spanish government since doping was not a crime at the time.

Spanish court 31 later cleared him and all the other members of Comunidad Valenciana of any involvement in the case.

On a document dated 28 July 2006 the court's secretary made clear none of the team members were found guilty of doping.

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