Southeastern Grocers LLC will close the Winn-Dixie at 7534 Beach Blvd. in June.
In a statement, Regional Vice President Shawn Sloan said the decision was not made lightly and said store associates are encouraged to apply for open positions in other stores.
The store is in the Beach Boulevard Shopping Center, at Beach Boulevard and Hogan Road.
Goldstein Commercial Properties said previously that the center was built in 1971 and renovated in 1996.
Property records show the store is almost 50,800 square feet in size.
Southeastern Grocers is based in Jacksonville.
The winndixie.com site says the company employs more than 38,000 associates in about 500 stores, 150 liquor stores and 280 in-store pharmacies in Alabama, Florida, Georgia, Louisiana and Mississippi.
Last year it converted seven Jacksonville Winn-Dixie stores into its Harveys Supermarket value brand.