Born in Soria, Castile and León, Bonilla began his career with hometown club CD Numancia, making his senior debut with the reserves in the 2008–09 season.
[1] In his second appearance with the main squad, on 16 May 2012, Bonilla was handed a start, and scored the third goal in a 3–1 win at Hércules CF.
[2][3] On 27 January 2015, after featuring in only one competitive match during the campaign, he moved abroad and signed for Greek Football League side Aiginiakos FC,[4] returning home on 27 August to SD Leioa of Segunda División B.
[5] In his first and only season for the Basques, Bonilla scored in the first leg of their 5–2 aggregate win over CD Olímpic de Xàtiva in the relegation play-off.
[7] Bonilla continued competing in the third division in the following years, representing RCD Mallorca (where he achieved promotion in 2018), UD Ibiza and Gimnàstic de Tarragona.