Muller-Wohlfahrt was established as the orthopaedic surgeon of choice for a number of leading sporting stars, including sprinting great Usain Bolt, and had worked at Bayern for more than 35 years by the time Guardiola was appointed as head coach in 2013.
The pair clashed frequently during Guardiola's tenure, with the former Barcelona boss irritated by Muller-Wohlfahrt's refusal to attend training sessions and reportedly clashing with the veteran physician over a number of issues, including treatment for the injury-plagued Thiago Alcantara.
Matters came to a head after Bayern's 3-1 defeat to Porto in the quarter-finals of the Champions League in 2015, as Muller-Wohlfahrt and three members of his staff stepped down and claimed they were held responsible for the defeat.
Bayern overturned the deficit in the second leg before falling short against Barcelona in the semi-finals, while Muller-Wohlfahrt is now back working with the club in a different capacity.
Nevertheless, time does not appear to have healed old wounds.
"I think Pep Guardiola is a person with a weak self-confidence who does everything to hide that from other people," Muller-Wohlfahrt said in an extract from his book, Seeing with your Hands: My Life and my Medicine, published in Bild.
"Because of that he seems to live in a constant fear. Not so much of defeats but of the loss of power and authority.
"He knew everything better: Five minutes warm-up had to be enough. But that couldn't end up well.
"Apparently he saw me as a receiver of commands whom he could order every time he wants."
Muller-Wohlfahrt explained he found himself yelling angrily at Guardiola as their relationship went downhill.
"I shouted at Guardiola and hit the table with my fist so hard that the plates and cups clanked. The first time during all the years [at Bayern] I had to be loud," he added.
Muller-Wohlfahrt's book features special guest contributions, including one from Uli Hoeness.
The Bayern president feels he could have prevented relations between the doctor and Guardiola deteriorating so badly, had he not been serving a jail term for tax evasion at the time.
"I think I would have been able to moderate the conflict between Mull and Pep Guardiola," Hoeness said.
"Pep Guardiola is a very proud Catalan, and the Spanish football coaches have a very different relationship with the medical department of the clubs.
"And Mull, on the other hand, is a very proud doctor who does not want to discuss his successful treatments. In the spring of 2015 two fronts immediately met.
"It lacked the buffer that I always was. There used to be similar scenes to the 3-1 defeat in Porto after lost games, more often than one would think."
Guardiola's City are two wins away from claiming the Premier League title and are in the quarter-finals of the Champions League. They are poised to be joined in the last eight by Bayern, who could wrap up a sixth consecutive Bundesliga crown this weekend.