The pair fell out when the Manchester City manager was in charge at Bayern.
"I absolutely could not let it go that a young trainer, who was very successful and probably one of the greatest in the world of trainers, meddled in the medical business and knew everything better than I did," recalled Müller-Wohlfahrt in an interview with BR24.
The biggest flashpoint came when the entire Bayern medical staff resigned after Guardiola blamed injuries for defeat to Champions League opponents Porto in 2015.
Müller-Wohlfahrt said at the time, "For inexplicable reasons, the medical staff is held responsible for the loss."
Today, the retired medic says: "We have met and it is all over. And so it is fine for me. We appreciate each other and he values my work. He has never questioned that at Bayern."