The Germany international is set to miss the next six months after suffering a recurrence of the significant injury 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 confirmed that he has suffered a major setback.
"Holger Badstuber has been in rehab once against 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.
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.