Muller-Wohlfahrt, the doctor for the German national team, is renowned as a world leader in the treatment of sports injuries.
In explaining his decision to leave Bayern, he suggested his medical department had been blamed for the club's 3-1 UEFA Champions League loss to Porto on Wednesday, which came with a host of Pep Guardiola's star players absent through injury.
"After the Champions League match of Bayern Munich against Porto the medical department was for some inexplicable reason made primarily responsible," read a statement from Muller-Wohlfahrt.
"The bond of trust is damaged."
Bayern media director Markus Horwick is quoted as telling Sport 1 that the club had "not been informed about this step".
Muller-Wohlfahrt, who has been associated with Bayern for almost 40 years, previously resigned his position in 2008 following a row with then-coach Jurgen Klinsmann, only to return when the ex-Germany international departed the club.
