Lewington hobbled off with a knock after 64 minutes of the Dons' 3-0 home win over Tranmere on Saturday.
Seven minutes later, the left-back was followed down the tunnel by midfielder Stephen Gleeson and on-loan striker Patrick Bamford.
"I didn't make one sub tactically," said Milton Keynes manager Karl Robinson. "They were all forced subs.
"It looks like ligament damage with Dean. Hopefully it will settle down. He is a wonderful healer so we will have to wait and see."
Gleeson has only recently returned from a three-month absence with a broken metatarsal, making his first start since mid-December against Tranmere following three substitute outings this month.
It was also Bamford's first start since the end of November following his hamstring problems.
Daniel Powell has missed the last two matches with a hamstring injury and he remains a doubt, while fellow winger Luke Chadwick will stay on the sidelines with his hip flexor problem.
David Martin (back) has returned to training but this match will probably come too soon for the Dons goalkeeper so Ian McLoughlin is expected to deputise for a seventh game.