The Mali forward was stretchered off ahead of the clash with Aston Villa after twisting his left knee during the warm-up and left the ground on crutches.
Sidibe will undergo further tests to ascertain the exact nature of the problem, but the club have concerns as he has only recently returned from several weeks on the sidelines having hyper-extended the same knee in December against Fulham.
Former Swansea and Gillingham player Sidibe admitted before the weekend that his knee was still causing him concern, but he was prepared to play on until the end of the season.
PainReserve team boss Mark O'Connor told The Sentinel: "Mama has twisted his knee. He went over and was in a lot of pain.
"I don't think anybody touched him, he just went over. I saw him after and he seemed a little better in himself, but once we get him looked at, we will know more.
"It could be that this is just a scare and he is fine by the end of the week. I honestly don't know, but I am just hoping he is all right."
Sidibe has scored just three league goals in 17 starts and five substitute appearances this season, but has played his part in Stoke's survival battle with his all-round contribution.
Meanwhile, fellow striker Henri Camara also missed the reserve clash after being allowed to return home to Senegal for personal reasons.