Muller-Wohlfahrt had been a member of the Bayern set-up for 38 years before quitting in 2015, although returned after Guardiola left but departed again last November.
Muller-Wohlfahrt wrote in his autobiography, which is being serialised by Bild: "Under Pep Guardiola, the climate changed at Bayern Munich, and it became more and more clear that he did not trust me and my team. On the one hand, he was totally uninterested in medical issues, but on the other hand, he demanded that we perform miracles.
"Guardiola was often portrayed in the media as an innovative, if not revolutionary, coach. But at Bayern Munich he turned the clock back tremendously. He even went so far as to turn our medically thought-out, well-rehearsed preparation program on its head before the actual football training.
"I simply could not reach Pep Guardiola with the way I think and work. Even my reports of injured players did not interest him. Whenever I wanted to talk to him, he immediately turned away and walked away.
"I think Pep Guardiola is a person of low self-esteem, who does everything in his power to mislead others. He therefore seems to live in constant fear, not so much in defeat, but much more in the loss of power and authority."