The retailer is now protected from its creditors, while it attempts to rationalise its finances.
Winn-Dixie, which lost US$399.7 million (£209.4 million) in the last quarter, has struggled to compete with Wal-Mart and other grocery chains.
The store group will be able to fund its continuing operations after obtaining US$800 million (£419.2 million) debtor-in-possession (DIP) financing from Wachovia Bank, replacing a previous US$600 million (£314.4 million) credit limit.
Winn-Dixie president and chief executive Peter Lynch remained bullish about the group's chances of recovery.
He added: 'I am convinced that the Chapter 11 process will give us the opportunity we need to restructure our finances, strengthen our business performance and achieve a sustained turnaround at Winn-Dixie.'
All 920 Winn-Dixie stores have remained open for business.