Mustafi was substituted in the 73rd minute of Arsenal's 3-0 triumph over Watford on Sunday, when the 6ft centre-back pulled up short with a groin injury. The former Valencia player scored the opening goal, marking his third for the Gunners this season.
Arsene Wenger confirmed after the game that Mustafi will be assessed ahead of their last-16 second leg against Milan on Thursday, while the Frenchman is also hopeful over the fitness of Hector Bellerin and Nacho Monreal.
"It's a groin problem. We don't know how bad. They told me they have to check tomorrow," Wenger told reporters in his post-match press conference.
"[Hector] Bellerin is in quite a good way, however. He could be available for Thursday. [Nacho] Monreal as well."
Arsenal beat Milan 2-0 at San Siro in the first leg of their Europa League round-of-16 fixture last Thursday.