Panera Bread (PNRA) reported third-quarter earnings after the bell on Tuesday that failed to impress. For the period ended Sept. 24, Panera earned a profit of $1.35 per share, excluding tax-related adjustments. That represents a 9% increase in earnings per share from the year-ago period and is in line with analyst estimates. However, revenue for the quarter clocked in at $572.5 million, which was significantly below Wall Street's estimates for total revenue of $584 million in the period.

The fast-casual cafe chain suffered a 1% decline in transactions at company-owned stores during the quarter, although that drop was partially offset by an increase in average check growth. During its third quarter, Panera successfully raised prices 1.7%, which demonstrates the company's branding power.

Nevertheless, Panera lowered its fourth-quarter guidance because of weak comparable sales. Management now expects fourth-quarter and fiscal 2013 EPS of $1.91 to $1.97, down from $2.05 to $2.11 per share. Shares of Panera were down as much as 3% in after-hours trading.