Cooper joined the Cherries from Portsmouth in the summer of 2005
Bournemouth quartet Shaun Cooper, Lee Bradbury, Brett Pitman and Ryan Garry have all agreed new deals.
The quartet were all out of contract and utility player Cooper, 24, had been linked with Crewe - but has signed a two-year deal at Dean Court.
"It's great news that he has decided his future is with us," Cherries boss Kevin Bond told BBC Radio Solent.
"I thought he may sign for Crewe, and I could understand his wanting to play at the highest level."
He continued: "I think Shaun sees that there are difficult circumstances at the club at the moment, but in the medium to long-term he sees that things are looking good at Bournemouth.
"It's a great credit to the chairman who worked extremely hard to get him, and everyone's delighted."
Bradbury, who has spent much of his career as a forward but finished last season with some impressive form as an emergency right-back, has signed a one-year deal to stay at the club.
Striker Pitman has agreed a deal to keep him with the Cherries until 2010, while Garry has agreed a new deal after missing most of last season through injury.
Cherries chairman Jeff Mostyn added: "Kevin (and I have worked extremely hard to secure new contracts in difficult circumstances.
"The players in question have sown us both great loyalty and this can only bode well for the new season."
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