On 18 March 2012, Trujillo made his first-team debut with the Andalusians, featuring the first half of a 1–1 Segunda División away draw against Real Valladolid.[3] On 27 May, he played his second game with the main squad and in the competition, a 1–0 away victory over former side Guadalajara.[4]
In June 2012, it was announced that Trujillo would be promoted to Almería's first team for 2012–13.[5] Despite missing the start of the season, he was handed a start on 8 September in a 3–0 away defeat against CE Sabadell FC,[6] but soon established himself as a regular due to Hernán Pellerano's legal problems,[7] and contributed 31 matches as they obtained promotion in the play-offs.[8]
On 12 July 2013, Trujillo renewed his link with Almería until 2017.[8] He made his La Liga debut on 19 August, starting in a 2–3 home loss to Villarreal CF.[9]
Trujillo scored his first goal as a professional on 2 March 2014, netting from a corner kick but in a 4–1 defeat at FC Barcelona.[10] On 7 August 2015, he moved to fellow top-tier club Levante UD after agreeing to a four-year deal.[11]
On 5 August 2016, after struggling with injuries and suffering relegation, Trujillo returned to Almería on a three-year contract.[12]