The company also is developing new recipes for its tortillas, which are the only items on the menu with artificial ingredients.

DENVER — After first announcing the initiative in 2013, Chipotle Mexican Grill has achieved its goal of moving to only non-bioengineered ingredients to make all of the food served in its restaurants in the United States, including its ShopHouse Southeast Asian Kitchen locations. The company also is developing new recipes for its tortillas, which are the only items on the menu with artificial ingredients.

“There is a lot of debate about genetically modified foods,” said Steve Ells, founder, chairman and co-chief executive officer of Chipotle. “Though many countries have already restricted or banned the use of G.M.O. crops, it’s clear that a lot of research is still needed before we can truly understand all of the implications of widespread G.M.O. cultivation and consumption. While that debate continues, we decided to move to non-G.M.O. ingredients.”

In March 2013, Chipotle became the first national restaurant company to voluntarily disclose bioengineered ingredients in its food and committed to eliminating them. Most of the use of bioengineered ingredients came from soybean oil, which the chain used to cook chips and taco shells, as well as an ingredient in the adobo rub for grilled chicken and steak. Chipotle’s corn and flour tortillas also contained bioengineered ingredients.

The company’s suppliers planted non-bioengineered varieties of corn, and the company replaced soybean oil with sunflower oil to cook chips and taco shells, and rice bran oil for other recipes and uses. Both oils are extracted from crops for which there are no commercially available bioengineered varieties. Other bioengineered ingredients in tortillas were replaced with alternatives.

Excluding tortillas, Chipotle said the food on its entire menu consists of 46 ingredients, most of which may be bought from any local supermarket, the company said. While already having made significant strides in reducing the number of additives in its tortillas, Chipotle said it is working to eliminate the remaining few preservatives and dough conditioners.

“The goal is to achieve a simple recipe with only a few ingredients, much like tortillas made in more traditional ways that include only wheat flour, oil, water, salt and a starter for flour tortillas, for example,” the company said. “Achieving this goal will be difficult and take time. Tortillas today are made very quickly and require the use of dough conditioners to give the tortilla the consistency that was once achieved by allowing the dough to rise slowly.”

In a partnership with its tortilla suppliers and the Bread Lab at Washington State University, Chipotle is working to develop a new system of making tortillas that allows the dough to rise slowly without the need for dough conditioners. The challenge will lie in keeping tortillas fresh without preservatives, the company said.

Initial taste tests of new recipes have been encouraging, but the company said it’s too early to predict when the new recipes will be served at Chipotle locations.

“We are changing the way people think about and eat fast food, and that means cooking with the very best ingredients — ingredients that are free of additives — but still serving food that is affordable, convenient, and most importantly delicious,” Mr. Ells said. “That’s really unusual in fast food, but that’s the quest we are on, and we continue to make progress.”