The restructuring is expected to reduce the company's debt by more than $500 million.
Three locations in Jacksonville and one in Orange Park, Florida will be part of the first group of closings, the company said.
According to Winn-Dixie's website, the retailer has locations in Florida, Georgia, Alabama, Louisiana, North Carolina, South Carolina and Mississippi.
Traditional grocery stores have faced increased competition from online retailers like Amazon in recent years.
Click here to find the list of all affected stores.
National Content Desk Editor Joy Johnston contributed to this report