He made his debut with its first team on 4 October 2009 in a La Liga match against Villarreal CF, playing the second half as the ten-man side eventually held off the hosts to a 0–0 draw.
[5] Baena quickly became an integral part of the main squad, alternating starts with appearances from the bench in his debut season.
[6] Baena was regularly used by manager Mauricio Pochettino in the following campaigns, often partnering another club youth graduate, Javi Márquez, in central midfield.
[20] On 1 May 2022, in the last group fixture of the AFC Champions League, he scored in injury time of the 2–2 home draw with Vissel Kobe, sending his team through to the knockout stage at the expense of Melbourne City FC.
[22] Baena won his only cap for the Spain under-21 side on 28 March 2011 as a member of Espanyol, coming on as a 70th-minute substitute for Athletic Bilbao's Ander Herrera in the 1–1 friendly draw with Belarus held in Alcalá de Henares.