Leverkusen. Three days before scoring his first Bundesliga goal, Ljuboja scored his first goal in the UEFA Cup in a 2–0 win over Rennes and scored a brace in a 2–0 win over P.A.O.K. At Stuttgart, he formed a striking partnership with Jon Dahl Tomasson. Later in the season, he scored eight goals and the club finished in ninth place. He was contracted in April 2006 (through 2009), but by that his income, that was still paid half by PSG, was lowered significantly. Although he had a valid contract, he demanded from Stuttgart the same wages he got before from PSG. Stuttgart in consequence told him to look for a new club in the summer of 2006 and let him train with their reserve team that played in the third German league. In August 2006, Ljuboja was transferred on loan to Champions League participant Hamburger SV for one year with the option to buy the player afterwards. Ljuboja made a good start by scoring on his debut, in the first round of DFB-Pokal, in a 4–3 loss against Stuttgarter Kickers; then, made his league debut in a 1–0 loss against Borussia Dortmund on 16 September 2006 and scored his first goal, a week later, in a 2–2 draw against Frankfurt. He also played six games with the team in the UEFA Champions League. At Hamburg, he was also demoted to the reserves team because he did not participate in team briefings. Hamburger SV did not use their option to buy him, so he went back to VfB Stuttgart at the end of the season. Upon his return, VfB Stuttgart was looking to offload him to another club and he was placed at the Stuttgart reserves. Ljuboja says that he wanted back to France, having desire to leave Stuttgart but to no avail. At the end of July, he was linked a move to Italian side Siena, but the transfer did not materialize. He was also linked with a move to Fulham, having been on trial. He was part of the reserve team of VfB Stuttgart in the Regionalliga. In January 2008, Ljuboja was loaned out to VfL Wolfsburg, until the end of the season, after training with the club. He made his debut, on 2 February 2008, in a 1–1 draw against Arminia Bielefeld; then one month later, he scored his first goal in a 1–1 draw against Hamburg. At