Çubukçu made his debut for Hertha BSC II in the 2005–06 Regionalliga season, making a total of five appearances. In the following season, he made 22 appearances. However, Hertha's second team were relegated at the end of the season. In 2007–08, Çubukçu helped his club to the league title with 12 goals and 11 assists, which earned him a place in the first team. He was initially allowed to practice there, but was not brought to training camp by coach Lucien Favre, after which he left the club for Turkey and signed a contract with Gençlerbirliği. After some strong initial performances, he became a reserve after a new coach was brought in, whereupon he terminated his contract by mutual consent with the club.
