Nelsen was dealt with another blow before the start of the 2006–07 season, with a serious hamstring injury forcing him out until the new year. On his return to the team in an FA Cup fourth round win against Luton Town, he was immediately made captain. In July 2007, he signed a new five-year deal with the club until the summer of 2012. He scored his first league goal for Blackburn with a header against Wigan Athletic on 26 April 2009 in a 2–0 win which helped Blackburn stay in the Premier League for another season. He then scored his second Premier League goal against Portsmouth with a header from a corner taken by David Dunn on 7 November 2009, and has also scored goals against Birmingham City and Fulham. On 11 April 2010, Nelsen came on for the injured Christopher Samba against Manchester United at Ewood Park in a 0–0 draw. Nelsen made his 175th appearance for Blackburn Rovers, leading the team in a 3–2 defeat to Everton at Ewood Park on 17 April 2010. In all competitions, Nelsen made a total of thirty-three appearances and scored four goals in the 2009–10 season.