Fontàs made his first team debut on 31 August 2009, replacing another "La Masia" graduate, Gerard Piqué, in the final six minutes of a 3–0 La Liga home win against Sporting de Gijón. Earlier into the 2009–10 campaign he was called by manager Pep Guardiola to the Spanish Supercup and UEFA Super Cup games, respectively against Athletic Bilbao and FC Shakhtar Donetsk, but finally did not make the bench on either occasion. He spent the vast majority of his first senior seasons registered with the reserves.