The company said in an earnings conference call that 40% of its restaurants still don't serve carnitas.
The Mexican-food company, which promises to serve "food with integrity," suspected its carnitas supplier wasn't raising the pigs humanely enough.
The incident shows Chipotle is sticking to its values.
But the pork shortage is also "a bad sign" for the company's future, writes Roberto Ferdman at The Washington Post.
Chipotle's incredible growth is proof that people will pay more for sustainably raised food without hormones.
"But the company's success has also been a lesson in how hard it is to scale the entirety of a business like Chipotle," Ferdman writes.
The company has dealt with meat shortages before.
Last year, Chipotle began serving "conventionally raised" steak in response to a global beef shortage.
The company said this wasn't an option for pork, which is raised less humanely.
"We would rather not serve pork at all, than serve pork from animals that are raised in this way," company spokesman Chris Arnold told The Post.
Chipotle is very successful, and it plans to grow even larger in the coming years.
But the pork and beef shortages show how difficult it will be to expand the business while standing by its ideals.