Walk through the front door of the Chipotle on 18th Street and 8th Avenue in New York's Chelsea neighborhood, and it doesn't look any different from any one of the chain's other 1,000-plus locations. Sure, you may notice that it's one of the few locations that serve margaritas (made with Patron, no less), and if you've got a really good eye, you'll catch that the kitchen is equipped with a steam oven and a flat-top instead of the standard grill. But here's the thing: The Chipotle on 18th and 8th may have the best-kept secret menu in the city. And the kicker? It's not a secret at all. Let me explain.

It's pretty easy to understand Chipotle's popularity. Do they serve authentic Mexican food? Not a chance. But do they have friendly service, and food that's tasty, crisp, and light, and actually tastes like it could have been made in a real kitchen instead of a factory—all served quickly and at a reasonable price point? You bet. That they've managed to do this while still maintaining a competitive price point and delivering on a promise of ethical food production practices is nothing short of astonishing to me.

And the feather in Chipotle's crown these days is Nate Appleman, the 2007 James Beard Rising Star Chef award-winner and Chopped star who until a few months ago was the chef at Keith McNally's Pulino's, where he was putting out some awesome pizzas and a legendary late-night burger.

For the past three months, the chef has been working the line at the 8th Avenue Chelsea location of the chain: constructing burritos, testing recipes, and brainstorming on ideas to help the company move forward while maintaining its "food with integrity" slogan. It's their test kitchen, see, and it's designed to help figure out how every other Chipotle location can be more effectively run and produce tastier food.

Nate's move to Chipotle has been criticized by a few as selling-out-to-the-man, but I'm in full support of his decision, particularly because after talking with him a few times, he seems 100% in concert with the Chipotle mission, much of it due to the birth of his son. ("When I was living in California, there were amazing taquerias, but you never know the source of the ingredients. That's when I started going to Chipotle with my son.") He seems to truly believes that what the chain is doing can change the foodscape for the better. It's a pretty noble cause, and that it's actually tasty to boot is more than just icing on the cake. "I actually eat a vegetable Chipotle burrito every day," Nate told us.

But hold on. Seriously? For just seven bucks and change you can get a James Beard award-winning chef to cook for you? We immediately headed out to multiple Chipotle locations for side-by-side tastings of every item on the menu.

Here's the thing: the braised meats that Chipotle stuffs their burritos with are all cooked in large commissary in Chicago where they're then packed sous-vide and shipped out to individual locations before being reheated and served*. At the Chelsea location, however, everything is made in-house from scratch—oftentimes starting with whole cuts of meat that are broken down on-site, a tactic Chipotle is exploring in order to be able to deliver on their humane-meat promises.

*For the record—anybody who's ever eaten carnitas or barbacoa at a Chipotle has eaten food cooked sous-vide. It's not just a fancy restaurant thing!

So you can still get the same burritos, bowls, salads, hard and soft tacos as they've got on every Chipotle's menu—but it's the subtle differences in preparation that make all the difference. On one visit, Nate is testing out a new chicken and pork chorizo recipe on the public, an 8 1/2-by-11" sheet of paper taped to the counter the only advertisement for the special.

"The carnitas at Chipotle are made with pork shoulder, but pigs only have two shoulders—what happens with the rest of that pig? We're trying to develop more recipes that utilize whole animals or alternative cuts," explained Nate. When I pressed him on what cuts of pork were going into the chorizo, I got a one word answer: pork. Yes, but what kind of pork? "Uh... it's... it's pork," he responded cagily. Apparently Chipotle holds their cards very close to the chest when it comes to their recipes.

The chorizo, by the way, is fantastic. Mildly hot with chilis with a nice hit of warm spices and a rich, crisp, fatty texture like the kind of good Italian sausage you'd want to crumble over your pizza. Cooked on a hot plancha, it develops a nice crisp browned crust. According to Nate, Chipotle is planning on replacing all of their grills with these high output flat-tops. About half of the locations in New York currently use them.

"We're not the only Chipotle with special menu items," Nate goes on to say. The location in Washington's Dulles airport* is experimenting with serving a full breakfast, including eggs and a potato hash made with a different version of the chorizo. Some Virginia locations source their meat from Joel Salatin's Polyface Farms and cook all of their carnitas in-house. Most locations try to source at least their vegetables locally, but none take their experimentation and ingredients-sourcing to the level of the Chelsea spot.

*EDIT: We originally falsely reported this as Chicago's O'Hare

Interestingly, the vast majority of customers here don't even notice the change. "We'll occasionally get someone who asks us why we're using brown rice instead of white, or why our salsa is different, but for the most part, people are just happy with the good food," says Nate. And they're happy with that—Chipotle's goal here is not to have one location that serves better food than anyone else, though that indeed is the welcome side effect of hiring a world-class chef to run a burrito joint. Unless you're looking for them, the differences are subtle: brown rice instead of white, a roasted tomato and tomatillo salsa in place of the pico de gallo, whole wheat tortillas sourced from a different supplier and soft corn tortillas upon request, to name a few.

Despite the fact that the basic recipes for the carne asada, adobo chicken, carnitas, and beef barbacoa are ostensibly the same as those used in the central commissary, there's a marked difference in the quality. Whether it's because of the equipment being used to prepare it, or because of Appleman's watchful eye, I can honestly say that their cooked meats are amongst some of the tastiest things you'll find in the city.

The carnitas in particular are remarkably juicy with the intense, porky flavor of the best confit. Rather than the shoulder clod used for the barbacoa at the standard Chipotle, Appleman is experimenting with short rib, resulting in meat that's juicier, richer, and cooked in a way that manages to be simultaneously completely tender yet still retain a bit of its structure.

On any given day, the carne asada might be made from any of a half dozen different cuts. Nate wouldn't disclose what the Chipotle standard is ("It's... uh, beef."), but at the Chelsea location, you'll find skirt, hanger, and flank in the rotation. It's also seared much better with distinct (and delicious) charring. Interestingly, on our last visit, Nate was also testing out a few new recipes for the Asian fast-food concept that the Chipotle team is developing. Unfortunately none of the test recipes were available for the public to sample.

In fact, asides from a rather bland faux-meat soy-based vegetarian offering, the only things we tasted that was not better than at a regular Chipotle were the beans. Both the black beans and the red kidney beans (which replace the standard pinto beans) were undercooked and still crunchy in the center. Oops.

Of course, Chipotle would rather you not really know about this. "We don't really like to advertise the fact that we're different," said Nate. His role is really to experiment with recipes, techniques, and preparation tactics in an effort to develop methods to improve the food at all of the other Chipotles nationwide. It's the Chipotle that Chipotle could be, and might well be the best food quality-to-the-dollar deal in the city.

For a full side-by-side, dish-by-dish comparison, click through the slideshow.

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