The 20-year-old sustained the knock on Tuesday, and a scan on his knee has since revealed that the defender will face up to nine months on the sidelines.
Dons manager Terry Brown admitted that it was frustrating to lose McNaughton, but claimed he could still play a key role in the first team next season.
He told the club's official website: "It is a blow for the lad, but I am sure he can recover and be a part of our plans next season."
The former West Ham player has made 20 appearances for the club since making his loan deal from Upton Park permanent in January.
He is joined on the sidelines by striker Charlie Strutton, who is out for three weeks with ankle ligament damage.
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