Returning to the scene of their famous 2012 triumph, the Blues need to overturn a 3-0 aggregate deficit if they are to advance.
The Blues enter the game on the back of a disappointing FA Cup final defeat to Arsenal, although they did seal a top-four finish in the Premier League.
Here, Sports Mole looks at how Chelsea could line up at the Allianz Arena this weekend.
Out: Billy Gilmour (knee), Cesar Azpilicueta (hamstring), Christian Pulisic (hamstring), Pedro (shoulder), Marcos Alonso (suspended), Jorginho (suspended)
Doubtful: Ruben Loftus-Cheek (knock), N'Golo Kante (fitness), Willian (knock)
If Chelsea's task was not difficult enough - no team in 92 attempts has recovered from a three-goal home first-leg deficit - they will have to do it without a number of players.
Christian Pulisic and Cesar Azpilicueta, two certain starters, pulled up with hamstring injuries against Arsenal and will play no part against Bayern.
Pedro was also stretchered off at Wembley with a shoulder injury, while N'Golo Kante has missed the last seven matches and Willian is carrying a knock.
To add to those woes, Jorginho and Marcos Alonso are both suspended for the second leg.