He played the full 90 minutes in the opening home draws against Spain and Serbia and Montenegro, followed by a substitute appearance in the away loss to Belgium. Misimović then enjoyed a spell as a consistent starter before being substituted 10–20 minutes into the second half, in the 1–1 home draw with Lithuania (scored the opening goal), the away win at San Marino, and finally the 1–1 draw against Spain in Valencia (again scored the opening goal before Spain tied deep into injury-time in the 96th minute). For the deciding four qualifiers (home win against Belgium, the away win at Lithuania, home victory over San Marino, and the away defeat to Serbia and Montenegro), Slišković dropped Misimović to the bench, bringing him into action only in the final 15–20 minutes of each tie. UEFA Euro 2008 qualifying began in fall 2006 with Slišković still team manager and 24-year-old Misimović an established starter and goalscorer. The opening match dismantling of Malta was followed by the shocking 1–3 defeat to Hungary at home that prompted Slišković's resignation, which he retracted a couple of weeks later and stayed on. Still, more disappointment was to follow with a 2–2 draw at lowly Moldova, as Misimović sparked a comeback that ultimately fell short by scoring a goal at 2–0 down. Four days later, Bosnia were heavily defeated 0–4 by Greece at home, forcing Slišković to resign for the second time in three months – this time for good. As the winter break in qualifying commenced, the Bosnian team was in crisis mode with relations inside the organization strained to the maximum. This led to thirteen Bosnian national team players (Misimović, Džemal Berberović, Vladan Grujić, Mladen Bartolović, Mirko Hrgović, Zlatan Bajramović, Saša Papac, Emir Spahić, Ninoslav Milenković, Ivica Grlić, Mirsad Bešlija, Kenan Hasagić and Almir Tolja) releasing what was reported as a signed joint statement in protest. Published in the "Dnevni Avaz" daily in late October 2006 as a press release, the statement announces the players' intention to boycott all national team matches until four FA officials – Milan Jelić, Iljo Dominković, Sulejman Čolaković, and Ahmet Pašalić – resigned.