The defender missed around 20 months of action after damaging knee ligaments in December 2012, and now faces another "long period" out after tearing tendons in his left thigh during Bayern's 2-0 victory over Stuttgart on Saturday.
But Badstuber, whose return to the first team lasted just three Bundesliga matches, says he is determined to recover as quickly as possible.
"I'm obviously very disappointed at the moment," the 25-year-old told the club's official website.
"But now I know how to deal with such a situation.
"Do not worry, I will come again. I will not give up."
Badstuber had played the full 90 minutes against Wolfsburg and Schalke before being forced off two minutes prior to half-time this weekend.
News of Badstuber's latest setback is a major blow to Bayern, who host Manchester City in the UEFA Champions League on Wednesday.
