The 24-year-old injured himself on Sunday when he twisted his knee in a pre-season training session and underwent investigation by a knee specialist, who determined he will need surgery.
New Werder coach Robin Dutt told German magazine Kicker: "That's too bad for Philipp Bargfrede, he had made a good impression on the first days."
Bargfrede only made 13 appearances for Werder last season following Achilles problems and an earlier knee injury.
He said: "It is totally aggravating for me. I was out in the winter after only a few days of training and now it happens to me again."