Badstuber trained with the squad for a while before continuing with an individual session, the club said.
The 26-year-old Germany defender, who suffered successive knee ligament tears that ruled him out for more than two years before his return to action early this year, suffered the latest setback in their Champions League 6-1 win over Porto in April.
Winger Arjen Robben has returned to training following his groin injury, sustained while on international duty last month, and Spaniard Juan Bernat was also declared fit on Wednesday after suffering an adductor muscle injury earlier this month.
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Bayern are top of the Bundesliga, seven points clear of second-placed Borussia Dortmund after winning all eight of their league matches so far. They also lead their Champions League group with two wins from two games.
(Reporting by Karolos Grohmann,; Editing by Neville Dalton)
