Shares of Chipotle Mexican Grill fell as much as 4 percent in aftermarket trading Thursday after the company missed on earnings.

The burrito chain posted 55 cents a share, falling short of analyst estimates of 57 cents a share, according to Thomson Reuters. Revenue of $1.03 billion was in line with expectations.

Sales at Chipotle's established restaurants fell 4.8 percent during the fourth quarter. In January, the company said that after plummeting 20 percent in October, comparable sales improved in the final two months of the year, as the chain faced easier comparisons from the prior-year period.

"In the upcoming year we intend to continue to simplify and improve our restaurant operations, utilize creative marketing to rebuild our brand, and further the roll-out of our digital sales efforts," Steve Ells, man CEO of Chipotle, said in a statement. "All three of these strategic initiatives are centered on improving the guest experience and restoring customer affinity for the Chipotle brand, and we are confident in our teams' abilities as we start this new year."

The company expects same-store sales to rebound and be in the high-single digit range in 2017.

Analysts still have plenty of doubt about the company's ability to recover from a string of foodborne illnesses that occurred well over a year ago.



"Turnarounds and recoveries of this nature take time," Nicole Miller Regan, an analyst with Piper Jaffray, told CNBC on "Power Lunch" ahead of Chipotle's earnings. "I think four to five quarters is very prudent and realistic and they are basically getting to the end of the timeline where people want to see things be a lot less worse."

The company disclosed that the rising cost of avocado and chopped tomatoes was a headwind for the quarter, but it was partially offset by lower beef costs.

During a conference call Thursday, the burrito chain said that avocado prices have begun to recover, however, it could face another problem with the popular ingredient.

As Chipotle tries to turn things around, its sales could be further dampened by a proposed 20 percent tariff on goods imported from Mexico, Mark Kalinowski, a Nomura-Instinet analyst, wrote in a research note Tuesday.

"Our belief is that the company generally obtains about 70 to 90 percent of its avocados from Mexico, all of its limes, the majority of its jalapenos, less than half of its tomatoes, and small amounts of other items (e.g., cilantro)," he wrote. "In other words, should a 20 percent tariff be enacted for goods imported from Mexico, Chipotle likely would bear the biggest brunt of this potential impact on food costs compared to the other companies we cover."

Piper Jaffray's Regan, however, doesn't see a possible tariff as an issue for the brand.

"I think, for them, the most important thing is a sales issue, not a cost issue," she said. "It's easy to take them in the darkest of days and isolate one more issue and layer it on to the already mounting issues. The fact of the matter is they need address revenues."