See main article: 2016 Torneo Internacional Challenger León.
Austin Krajicek and Rajeev Ram were the defending champions, but only Krajicek chose to defend his title partnering Alejandro Falla. Krajicek and Falla withdrew before playing a match.
Santiago González and Mate Pavić won the title, defeating Sam Groth and Leander Paes 6–4, 3–6, [13–11] in the final.