Born in Hamburg, he made his first appearance as a Hamburger SV player in a Bundesliga match on 11 August 2007, being sent on as a substitute in the 69th minute against Hannover 96.
On 18 May 2011, he signed a three-year contract with Bundesliga side 1. FSV Mainz 05 on a free transfer from Hamburg.
Choupo-Moting enjoyed a successful debut season with the club, scoring ten times in the Bundesliga. However, he missed most of the 2012–13 season through injury and was therefore unable to make an impact.