Nelsen signed a two-year contract extension with Rovers in late January 2011 which would keep him at the club until the summer of 2013. Under Steve Kean as manager following the sacking of Sam Allardyce, Nelsen was relieved as team captain of Blackburn in favour of Christopher Samba, Nelsen moving to vice-captain. Nelsen suffered a knee injury forcing him to miss the rest of the 2010–11 season. Following the 2010–11 season, in which Blackburn avoided relegation, Nelsen recovered from the knee injury and made one appearance against Aston Villa in a 3–1 loss.