Thiago Alcântara will miss Bayern's German Cup final as well as the World Cup for Spain after tearing a ligament in his knee.
Thiago had been out since March with a different ligament injury in the right knee.
"This is bitter for Thiago and I feel sorry for him," said the Bayern chief executive officer Karl-Heinz Rummenigge in a statement.
"A young man who wanted to come back at the World Cup and suddenly his dreams are burst. We will take care of him now and make sure he is fit at the start of the season."
Via Reuters