Panera Bread (NASDAQ: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.

Fool contributor Tamara Rutter owns shares of Panera Bread. The Motley Fool recommends and owns shares of Panera Bread. Try any of our Foolish newsletter services free for 30 days. We Fools don't all hold the same opinions, but we all believe that considering a diverse range of insights makes us better investors. The Motley Fool has a disclosure policy.