Wallace's did not call for the bankruptcy filing, Costie said. The decision was made by the Co-op's former management.
The filing will not affect the current management of the store, Costie added.
Neither the Co-op nor the Yale Bookstore is the official bookstore for Yale, according to the university.
But Yale is a creditor in the bankruptcy because the Co-op owes the university money in back rent.
The Yale Co-op's financial difficulties resemble the financial troubles the Harvard Coop went through four years ago, said Allan Powell, the Coop's corporate general manager.
"We were operating with a department store model," he said. "A lot of things had changed. People wanted more of an academic bookstore."
The Coop hired Barnes & Noble to manage day-to-day operations of the bookstore, with an agreement to keep it running as a cooperative.
The Coop has remained profitable for the past few years, giving rebates to members that reflect its profits.