The 32-year-old former England international faces surgery on a problematic knee cartilage.
Beattie has started just one Premier League game this season and has been linked with a move away from Stoke, following a bust-up with manager Tony Pulis in December.
Pulis said: “James has just had an operation to have a knee meniscus cleared up. He’ll be six weeks out. We’ve got two months left so it’s all about his rehab now.”