The German giants have made an unusually poor start to the current campaign, having drawn two and lost one of their opening seven matches, and they already sit five points behind Bundesliga leaders Borussia Dortmund.
Bayern opted to part company with boss Carlo Ancelotti after they were beaten 3-0 by big-spending Paris Saint-Germain and they have drafted in Heynckes as a replacement.
The 72-year-old, who has taken charge for the fourth time in his managerial career, has been handed a deal until the end of the campaign.
Muller expects that Heynckes will be able to improve the club’s performances but insists it won’t happen overnight and has called on the fans to be patient.
"We should be very careful about setting targets which we can throw into the bin afterwards again," Muller said.
"We won't suddenly play football from another galaxy. There will of course be matches where people see us and be very critical."