2006–07 season, Pedersen seemingly struggled for form during the early half of the league season, but returned to form in the second half of the campaign. With new management under Paul Ince in 2008, Pedersen found himself in and out of the team, but when Ince was dismissed in December 2008 and Sam Allardyce was appointed Pedersen regained a regular starting position. He has been frequently used a central attacking midfielder under Allardyce, initially with great success. On 17 April 2010, Pedersen, was poked in the cheek and then the eye from Everton midfielder Mikel Arteta, who acted angrily after Pedersen had tackled him in a challenge. They both were booked for stopping play. After a year of transfer negotiations, Blackburn announced that Pedersen had signed a new four-year deal at Ewood Park on 19 May 2010, which would see him stay contracted until the summer of 2014. He went on to make more than 30 appearances for them, and scored three goals in the 2009–10 Premier League campaign, in which Blackburn finished 10th, achieving 50 points and winning 10 league games at home and three away. Blackburn chairman, John Williams, who completed the formalities of the deal, added: "Sam made this, together with finding a striker, being our summer priority. "He regards Morten as a key member of the Rovers squad and his future at Ewood Park is now secure." On 6 November 2010, he scored a 40-yard free-kick against Wigan Athletic, in a 2–1 victory at Ewood Park, playing the full 90 minutes. And then four days later, on 10 November, he netted against Newcastle United at St James' Park, scoring in the third minute with his right foot following an assist from teammate Brett Emerton and he also took a punch to the stomach by Joey Barton. This was also coincidentally his 40th goal for the club in all competitions. On 21 November, in the game against Aston Villa, he scored twice at Ewood Park. First, from a free kick on the stroke of half time and the second came from a deflection off Ryan Nelsen's shot in the 66th minute. Rovers went on to win the game 2–0. At the end of the 2010–11 season, he had made 39 appearances and scored four league goals for Rovers in all competitions. On 13 August 2011, Pedersen started against Wolverhampton Wanderers at Ewood Park in a 2–1 defeat