"We are in the business of letting people make good choices about their food. Let's give it to them. If you're embarrassed about what you are serving, maybe you should change your food instead of trying to hide it," he said in an interview on CNBC's "Squawk on the Street."
Panera recently announced that it would be removing 150 additives from its menu, in an effort to continue its pledge to serve healthy food.
"The reality is there are a number of items on the Panera menu, not a lot, that have high salt levels or that are indulgences and you know what, that is OK as long as you are clear, you're making that choice, you're aware of it and you have the ability to make it on your own," he said.
The company banned trans fats in 2006 and has been offering chicken free of antibiotics since 2004. Shaich does not think that the move to offer healthier food will cause prices to go up beyond regular inflation.
"I am in favor of those regulations and I believe we may be the only restaurant company that is. We believe in transparency," he said.