In a professional career that lasted 14 years, he amassed La Liga totals of 122 matches and 14 goals over seven seasons, representing in the competition Numancia, Betis, Osasuna and Levante.

During his time at the Andalusia side, Juanlu also had a loan stint at Alicante CF in the Segunda División B. Juanlu made his La Liga debut in the 2004–05 campaign, playing 27 league matches for CD Numancia (two goals, scoring against Real Betis in the league opener on 28 August, in a 1–1 home draw)[1] before moving to Betis upon Numancia's relegation.

In late December, however, whilst playing against Deportivo de La Coruña in the Copa del Rey, he suffered fibula and ankle ligament fracture after a challenge by Borja, going on to be sidelined for three months.

[13][6] Late into the season he, alongside Sergio Ballesteros and Gustavo Munúa, was accused by teammate José Barkero of lack of commitment during a 0–4 home loss to Deportivo, which led to several match fixing allegations.

[14][15] On 27 August 2013, aged 33, Juanlu moved abroad for the first time in his career, joining compatriot Jonan García at newly promoted Greek club Kalloni FC.