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In the build-up for the 2012–13 season, Barcelona manager Tito Vilanova notified Afellay of his decreased playing time in the upcoming year. It prompted him to accept a loan offer from FC Schalke 04 on 31 August. He was reunited with Jefferson Farfán and coach Huub Stevens. Afellay made his debut the next day against FC Augsburg. He scored four goals at Schalke, including the opening goal in the Revierderby against Borussia Dortmund (1–2) and a goal against Arsenal in the Champions League. Afellay played his last Schalke match on 10 November; he picked up a muscle injury in a Dutch national team friendly against Germany a few days later. The injury prevented Afellay from playing until January, when he suffered a similar muscle strain in a friendly against Al Sadd SC. With the recovery this time taking the remainder of the season, Afellay returned to The Netherlands after expressing his discontent with the medical treatment at Schalke 04. Although both parties kept in contact, Afellay did not return to Gelsenkirchen anymore after the injury; a move that led to criticism from Schalke's general manager Horst Heldt.