The veteran striker will depart when his contract expires at the end of the season.
Müller, 35, joined Bayern Munich in 2000.
He has only represented the German giants since then.
Now Müller confirmed via a post on Instagram that there will be no extension - and thus his stay at Bayern Munich will end this summer.
"After a lot of speculation recently, I want to take the opportunity to clarify a few things for you. Even after all these years, no matter how many minutes I play, I still have fun on the pitch with the guys and when we fight for titles together. I could have imagined this role next year too," writes Müller.
The 35-year-old is also clear that this decision comes from the club.
"The club has deliberately chosen not to negotiate a new contract with me for next season. Even though it was not what I wanted, it is important that the club does what it believes is best," he writes.
There have been recent rumors that Müller could end up in MLS, with FC Cincinnati and San Diego FC being mentioned as potential destinations.
Müller has accounted for a total of 247 goals and 273 assists in 743 competitive matches for Bayern Munich.