The Red Devils were linked with a host of players in the summer transfer window as Mourinho looked to try and bolster his squad ahead of his third season in charge of the club.
Boateng was one defender that Manchester United were thought to have their eye on as Mourinho aimed to add to his squad before the start of the new campaign.
However, the 30-year-old opted to stay at Bayern Munich, despite the interest from Manchester United and French champions Paris Saint-Germain.
Now, the defender has revealed that he called Mourinho to inform him of his decision and explain why he opted to stay with the German side beyond the summer.
Speaking in an interview with German newspaper Bild, Boateng said: “I feel well at Bayern. It’s one of the biggest clubs in the world.
“I called Jose Mourinho, I told him that his interest was an honour for me and thanked him for trying so hard for me.
“I explained to Jose that it’s difficult to leave Bayern, and if I do, everything has to be in place to top this club.”
Meanwhile, Manchester United will return to Premier League action on Saturday evening when they travel to Watford in the top flight.
The Red Devils have endured a mixed start to the new season, with Manchester United having won two and lost two of their opening four games.
They are aiming to challenge for the Premier League title and be one of the main contenders as they look to win the trophy for the first time since 2013.
MORE: Man United latest news
MORE: Arsenal latest news
MORE: Chelsea latest news
MORE: Liverpool latest news