The 21-year-old Germany international, poached from Bundesliga rivals Borussia Dortmund for 37 million euros in a high-profile transfer, had missed the end of last season including Dortmund's Champions League final defeat by Bayern.
"I am happy to finally train with the team," Goetze said before signing dozens of autographs for Bayern fans. "I could not do too much today as it was not a long session."
Goetze agreed to the deal in April, on the eve of Dortmund's semi-final first leg over Real Madrid, triggering angry reactions by Dortmund fans, furious at a player who had joined the Ruhr Valley team as an eight-year-old.
An injury in the second leg ruled him out of any more games while also avoiding an awkward Champions League final clash against his future employer in May.
"Whatever I can do with the team, I will be doing with the team and then I will work individually to catch up," he said.
Bayern, who lost 4-2 in the German Super Cup to Dortmund last week, kick off their season on Monday with a German Cup first round against lower-tier SW Rehden before the Bundesliga starts next week.
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- Borussia Dortmund