Chipotle is still struggling to recover from its E. coli scandal

Chipotle is still struggling to recover from its E. coli scandal.

The fast-casual burrito chain reported that its sales and profit continued to fall compared to the same period a year ago, before the outbreak that caused the company to shut down dozens of stores.

Chipotle's sales dropped 16.6 percent to $998.4 million in the second quarter of 2016 compared to the same period last year. The outbreak began in late 2015, and the company finally got the all-clear from the Centers for Disease Control in February 2016.

Profit also declined sharply based on the same time last year, but showed improvements compared to the beginning of 2016.

The revenue decline hit despite the opening of 58 new restaurants in the past quarter.

Chipotle has struggled to regain public trust after E. coli scares rocked its restaurants across the country in 2015. In a call with investors Thursday afternoon, Chipotle executives said they were committed to restoring customers' confidence and that they invested more heavily than ever in marketing in the first half of 2016.

Chipotle introduced the rewards program Chiptopia this summer as part of that effort to win back customers. Although the program has been successful in drawing repeat visitors, the average check was down 3 percent during the month of July.

The company also acknowledged in its earnings call the indictment of its former vice president Mark Crumpacker in a New York cocaine bust.

Chipotle stock was down 2.2 percent in after-hours trading Thursday.

"Our entire company is focused on restoring customer trust and re-establishing customer frequency," CEO Steve Ellis said in a statement.