Speculation gathered pace over the last week when the 24-year-old was spotted in Spain, but the German international has insisted that his visit was "for personal reasons".
"I was in Barcelona for personal reasons, but these things immediately appear online nowadays," Muller told Sky90.
"Of course, it is flattering when you're being linked to a club like Barcelona. I am very happy at Bayern, though.
"Bayern mean a lot to me and have a place in my heart. I hope to stay at Bayern for many more years to come."
Muller, who has scored nine times in 16 games this season, won the Champions League and a domestic double with Bayern last season.