On 11 June 2015, Guadalajara announced they had signed Cota on loan in order to create competition with José Antonio Rodríguez, after club veteran Luis Ernesto Michel was sold to Dorados de Sinaloa. Cota then quickly rose to be the first-choice goalkeeper after his performances in the Copa MX, becoming champion after defeating Monarcas Morelia the Copa MX final, and became a key figure in the club's twelfth Liga MX title win against Tigres UANL. He was named in the Best XI of the tournament and won the Golden Glove award for the season.