Guardado scored his first goal for the "Che" on 12 May 2013, contributing to a 4–0 rout at Rayo Vallecano, and he featured mostly in the backline the following months. On 30 January 2014, Bundesliga club Bayer 04 Leverkusen announced that they had signed him on loan for the rest of the season, with an option to buy afterwards. He made his debut on 2 February in a 0–1 loss against 1. FC Kaiserslautern for the DFB-Pokal, playing as a left wing-back.