In 1993, Au Bon Pain Co. purchased the Saint Louis Bread Company, which was founded by Ken Rosenthal. At the same time, the St. Louis Bread Company was renovating its 20 bakery-cafés in the St. Louis area.

In May 1999, to expand Panera Bread into a national restaurant, Au Bon Pain Co. sold its other chains, including Au Bon Pain, which is now owned by Compass Group North America. Au Bon Pain Co. then renamed itself Panera Bread. The company operates or franchises 1,272 Panera Bread bakery-cafés in 40 states and 17 facilities that deliver fresh dough to the bakery-cafés every day. Panera Bread's CEO is Ron Shaich.

In its headquarters city of St. Louis, Panera Bread still operates under the name St. Louis Bread Company. The St. Louis metropolitan area has over 50 locations.

In 2005, Panera ranked 37th on BusinessWeek's list of "Hot Growth Companies", earning $38.6 million with a 42.9% increase in profits.

Panera Bread expanded into Canada, beginning in 2008 with Richmond Hill and Mississauga, both in the Toronto area.

On January 25, 2008, a class action lawsuit was filed against Panera Bread on behalf of investors who bought company stock between November 1, 2005 and July 26, 2006, alleging that Panera Bread failed to disclose material adverse facts about the company's financial well-being, business relationships, and prospects.

In a 2008 Health magazine study, Panera Bread was judged America's most healthy fast food restaurant.

In 2009, the restaurant review service Zagat named Panera one of the most popular restaurants for eating on the go. Panera was also rated #1 for Best Healthy Option, Best Salad, and Best Facilities, among restaurants with less than 5,000 locations.

Most locations offer free wireless Internet (Wi-Fi) access to customers. Panera operates the largest free wireless network in the United States. This service includes SonicWALL Internet filtering, which queries a central database before blocking or allowing access by category; the filter has been known to incorrectly categorize sites. Many locations restrict the duration of free wi-fi during peak hours to 30 or 60 minutes.