The Armenian was arguably Arsenals standout player in the 2-1 defeat at Old Trafford but was substituted in the 76th minute after another knock to his knee.
Arsene Wenger was hopeful that the injury was not serious and the midfielder has joined up with his team-mates in training on the eve of the second leg against Atleti.
David Ospina, who had been struggling with a rib problem, was also present at London Colney on Wednesday.
Wenger is yet to confirm whether Ospina or Petr Cech will start between the sticks for Arsenal at the Wanda Metropolitana.
Asked about Arsenals injury concerns following Sundays defeat to United, Wenger responded: Mkhitatryan had a little knock on his knee.
Ospina has a rib problem and [Alex] Iwobi has a hamstring problem.
The Frenchman hinted that Konstantinos Mavropanos could start on Thursday night after impressing against the Red Devils.
Mavropanos in training has shown top quality, Wenger said.
Can he show that in a big game? You never know. I think he did. He surprised everyone by his quality today.