The Bundesliga champions have announced that the Germany international has gone under the knife and now faces a lengthy recovery process
The 24-year-old first suffered a knee ligament injury in December 2012 and it was announced at the weekend that he had suffered a relapse of the same problem.
Bayern insist that the injury is not career-threatening, but Badstuber nonetheless faces another lengthy spell on the sidelines.
"On Monday 20 May 2013, Dr. Richard Steadman performed surgery on Holger Badstuber in Vail, Colorado. Due to extensive ruptures, the player’s cruciate ligament is no longer functional and was removed," a Bayern statement reads.
"Before the cruciate can be reconstructed using a surgical tissue graft replacement, the incisions and holes from the original op must heal completely.
"Until then, Holger Badstuber will maintain his physical fitness in sports rehab. The doctors in charge of the case estimate the player will be fit again in around 10 months. The injury is not career-threatening."
Badstuber is a product of the Bayern youth academy and has made over 100 Bundesliga appearances for the Bavarians since making his first team debut in 2009-10.