Bonilla scored his first goal for Alianza FC against Atlético Marte on 13 August 2011. He scored both goals against Águila on 11 September 2011, the match ended 2-1 to Alianza. He scored the only goal against Juventud Independiente on 2 November 2011. On 27 November 2011 he scored a 54th minute equaliser against C.D. Luis Ángel Firpo the match ended 1-1. On 22 January he scored the winning goal against Juventud Independiente in the 60th minute, the match ended 2-1. On 5 February 2012 he scored the first goal in a 3-1 defeat against C.D. Águila.
Bonilla's debut for El Salvador came against the All Whites (New Zealand) away from home (23 May 2012) in a 2-2 draw, coach Ruben Israel gave credit to Nelson Wilfredo Bonilla, who was playing with the national team for the first time, for helping to create opportunities for Rafael Burgos. Bonilla scored in the 16th minute for El Salvador against Moldova (27 May 2012), his team went on to win 2-0.