In his first season for FC Luzern, Lustenberger succeeded in integrating himself into the team. He earned increasingly more respect from manager Ciriaco Sforza, and by the winter break, he had earned a spot in Luzern's starting eleven.
In August 2007, Lustenberger transferred to Hertha BSC in the Bundesliga for 1.5 million Euros. In his first season with Hertha, he made 24 Bundesliga appearances. He scored his first Bundesliga goal during a Hertha 2–1 loss to 1. FC Nuremberg in December 2007. Although he was never a consistent starter, Lustenberger earned 37 caps over the two seasons that followed, and stayed with Hertha when the club was relegated to the 2. Bundesliga at the end of the 2009–10 season. During the 2010 summer break, he sustained an injury that ruled him out for almost four months. In his first game back, Lustenberger was forced to play the last eight minutes as goalkeeper, following the ejection of Marco Sejna.