He scored his first goal for the club in 3–3 pre-season draw with Newcastle United on 5 August 2006. However, on 18 August 2006, Pires damaged the cruciate ligament in his left knee in a friendly match against Cádiz and required corrective surgery to alleviate the problem, which kept him out of action for seven months in his new club in Spanish top flight. Pires finally recovered from knee injury and made his first league appearance for Villarreal as a second-half substitute when he was named in Villarreal's squad to face Real Sociedad on 17 March 2007. Pires scored his first league goal on his return from injury in a 3–3 draw away to Real Betis on 31 March 2007. After three appearances as a substitute, Pires made his first start for Villarreal on 22 April 2007 against Barcelona. He opened the scoring for his team to defeat league leaders Barcelona 2–0, avenging his premature departure against Barcelona in the Champions League Final the previous May.