Mondragón transferred from Istanbul to 1. FC Köln in May 2007. After arriving at his new club, he was forced to compete with established Köln goalkeeper Stefan Wessels for a spot in the starting eleven. One of the reasons that he chose 1. FC Köln it was because the current coach Christoph Daum was working there. After an intense pre-season, Mondragón was named as the new number one for 1. FC Köln. This resulted in Wessels leaving the club for Everton in England. Since Wessels departure, Mondragón established a first choice goalkeeper for the club until Mondragón was relegated to the bench after an altercation with Zvonimir Soldo over his desire to go on international duty. This resulted in Mondragón being sent home from the team hotel and being replaced by young Croatian stopper Miro Varvodić. His contract with Köln was terminated with effect from 31 December 2010, the reason being Mondragón’s desire to play in the MLS.