The 22-year-old has become a key player at The Reebok since joining from Birmingham two years ago.
His new deal will keep him at Bolton under the summer of 2014.
And the England Under-21 international, who was two years into the four-year deal he signed when he joined Wanderers, is now looking forward to staying in the north-west for the long term.
"I'm happy, my family is happy - everybody is happy," he told the club's official website. "The football club have been very good to me since the moment I signed here.
"I don't have any reason to want to move anywhere else and I'm looking forward to the upcoming season.
"The manager believes in me and says that I'm part of his plans, and I want to give my best to the club for the fans."
Muamba has made 83 appearances for the club, scoring one goal.
He was signed for Bolton by Gary Megson, but has become a favourite of current boss Owen Coyle, who was delighted to tie him down on a new deal.
"Everybody knows my opinion of him," Coyle said. "He's a great young prospect and I'm delighted he's signed an extended contract.
"He loves being at the football club, I like working with him and hopefully we can move on together."