Subsequently, Universidad played as feeder club to Unión Deportiva, after one of its founders and then chairman, Alfredo Morales, decided to merge after being installed into the latter's board of directors.
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On 27 October 2010 he made his official debut for Atlético, replacing Raúl García in a 5–0 win at Universidad de Las Palmas CF for the campaign's Copa del Rey round-of-32 first leg; two weeks later, as everything was already decided, he started in the second match, a 1–1 draw at the Vicente Calderón Stadium.
Hence, Juanito fell further down in the defensive pecking order, only appearing in a Spanish Cup match against Universidad de Las Palmas CF (1–1 home draw, after a 5–0 away win in the first leg); on 11 January 2011 he rescinded his contract with the club, moving to Real Valladolid in the second level shortly after.