The France international's previous deal was due to expire at the end of this season.
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Upamecano's situation led to talk of interest from the likes of Liverpool, PSG and Barcelona.
But the 27 year-old centre-half has now committed to a new deal with Bayern through to 2030.
Upamecano, who joined the team in Munich in the 2021/22 season, has won three Bundesliga titles and one German Super Cup.
He said, I’m really happy to be staying at Bayern and continuing to play in this team. We’ve got a great team and a great coach.
"We’ve got big goals together. In life, it’s always about mentality. I give my all for my teammates, in every training session, want to keep a clean sheet in every game and want to win as many titles as possible with Bayern.”