JACKSONVILLE, Fla. — Winn-Dixie Stores Inc. chairman, president and chief executive officer Peter Lynch will step down from those positions later this year.

Winn-Dixie Stores Inc. chairman, president and chief executive officer Peter Lynch will step down from those positions later this year.

Lynch, who has led the supermarket chain since December 2004, says he will resign after Winn-Dixie’s merger with BI-LO LLC is completed.

The transaction is expected to close between 60 and 120 days after the announcement of the deal, which was made on ­December 19.

In an internal letter to employees, Lynch said that Randall Onstead, chairman of BI-LO, will become the president and CEO of the combined company.

However, Lynch says he will stay on for an undetermined period of time to assist with the transition.

"Randall understands the grocery business, and more importantly, deeply appreciates Winn-Dixie’s strengths and the opportunities ahead of us to build on our successes and realize our goals," Lynch said in his letter. "He also shares my passion for this business, our guests and creating a winning team with you. I am confident that Winn-Dixie will be in good hands."

During Lynch’s tenure at Winn-Dixie the company has faced some significant challenges.

Three months after he took the helm in late 2004 Winn-Dixie filed for Chapter 11 bankruptcy protection. In an interview Lynch later described the company’s state as “tarnished, not broken.”

He then immediately set out to rebuild Winn-Dixie’s management team and took the chain in a new direction.

Prior to its bankruptcy filing the company had been locked in an unsuccessful struggle to be the low-price grocery of choice. The new strategy and positioning, first formulated as “fresh and local,” featured store remodels that emphasized quality perishables departments.

In his resignation letter Lynch noted that about half of the store base has been remodeled with "a transformational store format that can compete with any store in America."

In leaving Winn-Dixie, Lynch says he feels he was able to restore some of the supermarket chain’s former luster and sees a bright future ahead.

"I want you all to know that I am very supportive of this merger and wholeheartedly believe that it is the next major accomplishment we will achieve together," he said in his letter to employees.