The additives removed include federally-approved artificial colors, sodium benzoate, sodium nitrite and sodium phosphate, the company said.
St. Louis-based Panera said it had reformulated 122 ingredients, resulting in changes to most of its bakery-cafe recipes. It has also partnered with more than 300 food suppliers to replace ingredients and change preparation methods.
The company sells items such as bread, soup and coffee under its Panera at Home brand.
Restaurant chains — including McDonald's Corp and Yum Brands Inc's Pizza Hut — had committed last year to remove artificial preservatives from some of their ingredients and menu items.