On 19 August 2012, in the league opener against Valencia, Pepe collided with Real Madrid goalkeeper Iker Casillas in the play that led to the visitors equalizing the score 1–1 (the final result). He was subsequently taken to hospital for observation, being released the following day. Amid feuds with Mourinho, Pepe lost his starting place to Raphaël Varane throughout the season and would end up getting into a scuffle with Atlético Madrid manager Diego Simeone from the substitutes' bench in the 2013 Copa del Rey Final.