The Red Devils centre-back has been in fine form for the club this season and arguably their best player, having scooped the Premier League Player of the Month award in November.
Maguire made his fourth Champions League start of the season on Tuesday night when United welcomed Bayern to Old Trafford.
He he was part of a defence that kept the German champions quiet for much of the first-half.
However, around ten minutes before half-time, Maguire appeared to pick up an injury to his left groin.
The England international then received medical attention and it looked as though he was willing to remain on the pitch.
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Despite this, Erik ten Hag opted to make a substitution, with Jonny Evans coming on to replace him in the 40th minute.
Despite this, Erik ten Hag opted to make a substitution, with Jonny Evans coming on to replace him in the 40th minute.
It's a blow on a night where United must win to stand any chance of reaching the last 16 of the Champions League.
Luke Shaw then went off at half time, however, it's not clear what the reason the left-back was taken off. Aaron Wan-Bissaka was brought on as his replacement.
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United eventually fell to a 1-0 defeat on the night, with Kingsley Coman's goal enough to split to two sides.
As a result, Ten Hag's side are out of the Champions League and out of Europe altogether as they finished bottom of Group A.
United will now face Liverpool at Anfield in the Premier League on Sunday, with their new injuries adding to club captain Bruno Fernandes' suspension.