[2][3] Mora started his coaching career in 2011 with Tijuana Reserves in the Mexican lower divisions, before becoming manager of Atlético Chiapas in 2014.

Between 2012 and 2015, he also served as an assistant coach at various Mexican clubs, including Querétaro, Atlante and Cafetaleros de Tapachula.

[5] In January 2017, Mora took the vacant manager position of the main JDT team after Mario Gómez left the club.

In April 2022, JDT, managed by Mora, became the first Malaysian team to reach the round of 16 of the AFC Champions League after defeating Ulsan Hyundai 2–1 at Sultan Ibrahim Stadium.

[8] On 6 October 2022, Mora returned to Mexico and became the manager of Liga MX side Atlas, replacing Diego Cocca.