Van Buyten, who has spent the past five years in the Bundesliga, has signed a two-year extension.
Muller has signed a deal until 2013 while Badstuber has extended his deal with Bayern until 2014.
“We are delighted to have been able to agree contract extensions with each of these three players,” said Bayern chairman Karl-Heinz Rummenigge.
“In the near future, we will also hold talks with the other players whose contracts are expiring at the end of the season to set the foundations for the future.”