The company, which has been a bright spot in the restaurant industry, delivered double-digit comparable restaurant sales in the first half of the year even amid price increases rolled out in the second quarter.
Net income in the third quarter rose to $130.8 million or $4.15 per diluted share from $83.4 million or $2.66 a share in the year-earlier period. Revenue increased 31.1 percent to $1.08 billion from $827 million a year ago.
Wall Street had forecast Chipotle to deliver earnings of $3.84 a share on $1.06 billion in revenue, according to a consensus estimate from Thomson Reuters.
Higher beef, avocado and dairy prices contributed to a rise in food costs at the chain. Still, the chain's restaurant level operating margin ticked 2 percent higher to 28.8 percent.