The Germany international is set to miss the next six months after suffering a recurrence of the significant problem that kept him out for much of this season
The Germany international first sustained the injury during the Bavarians' 1-1 draw with Borussia Dortmund in December.
He was ruled out for the rest of the 2012-13 campaign but was expected to be back in time for next season, but the club have confirmed that he has suffered a major setback.
"Holger Badstuber has been in rehab once again and suffered a torn cruciate ligament injury in his right knee, and so has been ruled out for even longer," a statement on the club's official website read.
Bayern sporting director Matthias Sammer pledged that the club would support the defender and said he has faith that the long spell on the sidelines will not affect his career trajectory.
"He has our full support and we will look forward [to his return]. He will be available for us in the future, but for now he has all the time he needs to recover," he told Sky Sports.
"I dont want to name a timeline, this is very unlucky for him. But he will come back and I believe stronger than ever, especially mentally."
The 24-year-old will undergo surgery for a second time to rid himself of the injury once and for all.
Badstuber has been limited to just 18 appearances in all competitions for his club this season, many of which were at left-back due to David Alaba's injury at the start of the campaign.