Franck Ribery (ankle) limped off during Bayern Munich's 3-2 win over Fortuna Dusseldorf on Saturday and is confirmed to miss the game, while Bastian Schweinsteiger and Jerome Boateng are suspended.
Jupp Heynckes is set to give starts to Luiz Gustavo and Xherdan Shaqiri against the Gunners, while Arjen Robben (calf) is a doubt after sitting out Saturday's match.
Arsene Wenger is set to name the strongest side possible having not had a fixture since March 3 but Nacho Monreal is again unavailable, meaning that Thomas Vermaelen will deputise at left-back.
The second leg may prove too soon for Bacary Sagna (knee) so Carl Jenkinson is likely to start, while Abou Diaby (calf) could return to the bench after sitting out the north London derby.
Reports emerged on Monday night that Jack Wilshere (ankle) is set to miss the game and potentially the rest of the season.
Bayern Munich's superb win at the Emirates Stadium in the first leg means that the Gunners have not beaten the German side in five Champions League encounters.
The Bavarians have conceded three goals at home in total the Champions League so far this season – a statistic that Arsene Wenger's side need to at least double in this game alone to go through.
Mario Mandzukic (pictured right) scored in the first leg, making him the 10th different player to net for Jupp Heynckes's side in Europe this term.
If Arsenal fail to progress, it will be the third year in a row in which they have crashed out at the last-16 stage of the tournament.
Only two sides – Ajax and Inter – have previously made it through after losing the first leg at home.
However, the competition has never seen a team turn around a two-goal home deficit