Arsene Wenger's side is 2-0 down after the first leg and without its first choice goalkeeper for the trip to the Allianz Arena to face the reigning European champions.
Arsene Wenger's men are 2-0 down from the first leg of their last 16 tie but will take confidence from its last visit to the Allianz Arena at this stage last year when they won 2-0, only to be eliminated on the away-goals rule.
Toni Kroos and Thomas Muller netted for the Bundesliga outfit at the Emirates Stadium after both sides had missed first-half penalties, while Arsenal saw Wojciech Szczesny red carded.
However, if Arsenal can match the result of last March, they will at least take the tie to extra time.
The north London club's Premier League form has faltered in recent weeks, but a 4-1 triumph over Everton on Saturday to reach the FA Cup semifinals could prove inspirational as it prepares to head to Germany.
"It was important of course for us to win [on Saturday] to put us on a psychological front in a good mind and we can be inspired by our focus, by our desire and go to Bayern with the same spirit," Wenger told reporters after the clash. "The statistics go against us at Bayern but let's make sure the performance goes for us, then we have a chance."
Winning in Munich is no mean feat - the runaway Bundesliga leaders have not lost at home domestically since October 2012.
However, a home defeat to Manchester City in the group stages of this season's competition goes to show that Bayern is not totally unbeatable on home soil, particularly when it comes to English clubs.
Xherdan Shaqiri, Thomas Muller and Franck Ribery all returned from injury to fire Bayern to a 6-1 thrashing of Wolfsburg in the German top flight Saturda and the three will undoubtedly be a huge boost to their chances of making it to the quarterfinals Tuesday.
Arsenal will be without the suspended Szczesny, while Jack Wilshere is sidelined for around six weeks after picking up a foot injury in England's friendly victory over Denmark at Wembley last Wednesday.
Aaron Ramsey (thigh) and Kim Kallstrom (back) are nearing a return but are not thought to be in contention, and Laurent Koscielny (hamstring) and Nacho Monreal (foot) remain doubtful.
Theo Walcott and Abou Diaby (both knee) are long-term absentees.