The discussions reportedly involved sporting director Christoph Freund and the player's representatives, with Bayern making clear that they remain pleased with Karl's development on the pitch.
The 18-year-old had attracted attention for reasons beyond his performances, prompting criticism from senior figures at the club. Honorary president Uli Hoeneß had publicly questioned aspects of his behaviour, while the player's agent, former Germany captain Michael Ballack, subsequently defended him.
The situation became increasingly prominent in the German media, with Karl's celebrations and activities away from football also attracting scrutiny. The club were keen to address the matter internally rather than allow the disagreement to become a continuing distraction.
According to Sport Bild, Freund used the meeting to reassure the player's camp that Bayern Munich remain satisfied with his progress. The intention was to draw a line under the recent exchanges and allow the teenager to concentrate on his football.
There has been little suggestion that Bayern have lost faith in Karl's ability. Indeed, his recent performances have provided a timely response to the criticism. He scored in the Champions League victory over Atlético Madrid before finding the net again in the 2-1 Bundesliga win away to Mainz on 7 November.
Freund had already offered public support before the Mainz fixture, emphasising that the club value Karl's personality as well as his ability. The sporting director has previously described him as a different character from many young players and said Bayern want him to retain that individuality.
The club's position is that the player's work and contribution on the pitch remain the main measures of his progress. Karl's recent goals have helped shift the discussion back towards his football, while his selection for Germany's senior squad has provided another indication of how highly his development is regarded.
The meeting with Freund appears to have eased tensions between the club and the player's representatives. Bayern will now want the attention surrounding Karl to return to his performances, rather than the debate over his behaviour.
At 18, Karl remains at an early stage of his career, but his growing role at Bayern means scrutiny is unlikely to disappear. The club's message, however, is that they remain confident in the player and want him to continue developing in Munich.