Muller on Tuesday signed a new two-year deal that will extend his 12-year association with Bayern’s first team to the summer of 2023.
The 30-year-old’s new contract came just four days after Bayern elevated Flick from his role as temporary to full-time manager on a three-year deal.
Bayern have a number of first team players who will be entering into the final year of their contracts next season.
The likes of goalkeeper Manuel Neuer, Jerome Boateng, David Alaba, Javi Martinez and Thiago Alcantara will all have their contracts run out in the summer of 2021 and are yet to agree new deals.
Nonetheless, Flick is hopeful of a positive outcome in contract negotiations between the players and the club.
Asked about prospective extensions for the quintet, Flick told a media conference held via Zoom: "These are also decisions that every player has to decide for themselves.
"In the past weeks and months, I have already explained how important Manuel Neuer, David Alaba or Thiago are to us.
"They have undergone enormous developments over the past six months and were real top performers. The club also noticed that and I hope that it goes in the right direction."
Bayern Munich were four points clear at the top of the Bundesliga table when the Coronavirus pandemic brought the season to a halt.
