Following the decision, one gun policy reform group cheered the decision.
"We are thrilled that after months of discussions between Panera and Moms Demand Action, Panera is taking a proactive position in favor of our families' safety by putting a new gun policy in place. Moms are the consumers-in-chief of our households and we will reward companies that take a stand for our families' safety. We urge other national companies follow suit," said Shannon Watts, founder of Moms Demand Action for Gun Sense in America, in an email.
Panera's move follows similar announcements from several other chains. Last year, Starbucks began asking diners to refrain from bringing guns in restaurants while Chipotle Mexican Grill said the same earlier this year after gun-rights advocates brought assault-style rifles into one of its locations. Sonic and Brinker International's Chili's have also issued requests about gun carrying at their stores.
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"I think this industry has attempted to figure out how it stands out of 'make a point' political battles by advocates on either extreme," Shaich said. "I think what we feel is we're trying to be respectful of people's rights while at the same time ensuring that Panera isn't the battleground for political statement."
When asked about potential alienation due to the request, Shaich said the chain's customer base hold a wide spectrum of opinions.
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"I think at its core people get the request to make this an everyday oasis and not make this a battleground for political opinion," he added.
—By CNBC's Katie Little