Jonathan terminated his contract with the Che after a loan with Córdoba CF in the Segunda División B.[4] He returned to the second tier afterwards, signing for Albacete Balompié and starting for the better part of his stint.[5][6][7]
In 2009–10, Jonathan had his first taste of top-flight football, joining Levadiakos F.C. in Greece but being released at the end of the campaign without making a single competitive appearance. He then returned to his country's division three, successively representing CD Roquetas[8] and Burgos CF.[9]
Again as a free agent, Jonathan returned to Greece and its Super League in the summer of 2012, with Veria FC. He made his official debut on 15 September precisely against Levadiakos, being sent off in the last minutes of the match following a second bookable offence but contributing to a 0–0 away draw with a series of saves, including one from the penalty spot.[10]
In July 2014, Jonathan moved back to his homeland and agreed to a one-year deal at Getafe CF.[11] He made his La Liga debut the following 8 February at the age of 33 years and 10 months, in a 2–1 home win over Sevilla FC.[12][13]
Jonathan left the club on 3 June 2015, after his contract expired.[14] Subsequently, he rejoined Veria for two seasons.[15][16]