"We believe it's unnecessary to open stores of this sort at a time of margin pressure," said Ron Shaich, the company's chairman and CEO, during its third-quarter conference call. In the fourth quarter, 60 to 65 new locations are planned for the chain, which currently operates 1,135 units across the country.

The margin pressure Shaich referred to was caused by increased labor and wheat costs and a shift in consumer taste toward less margin-friendly menu items. The chairman also spoke about a weak performance by Panera's highly-pushed "Crispani" pizza offering and said it needs to have more sales or the company will drop the item.

Same-store sales at Panera restaurants during the third quarter, which ended Sept. 26, rose 2.6% year over year. At company-owned units, which make up 42% of its locations, they rose 3.4%, while franchise-operated majority of stores were up 2.1%. The chain's total revenue shot up 33%, to $273.2 million from the same year-ago period, while net income increased by $1 million, to $12 million.