Malouda was unable to secure a transfer away from west London and has been training with the Under-21s as a result. However, Di Matteo insists that the this situation is very different to what happened last year under Andre Villas-Boas, when Nicolas Anelka and Alex were forced to train separately.
"They have accepted the decision that has been made by us, and they're just going to focus on their targets for this season," Di Matteo told Sky Sports News.
"Over the past, there's been some expression of the player to part company, but it hasn't happened.
"So we've moved forward, brought in other players and they're the ones we're going to work with this season.
He added, "It was a combined decision between me and the club. It's obviously not an extremely positive message or decision for him, but I guess, at the end, we have to look after our own interests and that's the decision we've taken."
When asked if Malouda will ever appear for the first team again, Di Matteo added: "I don't know, only the future will tell. But he's with the Under-21s.
"The transfer window doesn't open again until January."