Smoky Chipotle Mac & Cheese

It only ranks third in America’s overall favorite comfort food (behind pizza and burgers), but here in the South, mac and cheese reigns supreme. It was the first dish I posted on Comfort du Jour when I finally got the nerve to start my blog and, as you can see, we enjoy making fun variations of it at our house! This simple, versatile side dish is like a blank canvas—you can apply so many flavors to it and, with all the different pasta shapes available, hardly ever have a repeat.

The main thing you need for super creamy mac and cheese is a velvety base, and for me, that means a bechamel—which is just a fancy French word that describes “white sauce.” Bechamel is one of the five so-called mother sauces, because it serves so many purposes. The key ingredients of a classic Bechamel are butter and flour (cooked together in equal parts), and milk. The fat in the butter coats the starch in the flour, and the resulting paste serves to thicken whatever liquid is added to it—in this case, milk.

This butter-flour magic is called a “roux,” and it’s one of the first things I remember really learning from time spent in my grandmother’s kitchen. When she first told me about this important technique, I thought Gram was calling it “Roo”—like Kanga’s baby from the Winnie and the Pooh books (that’s how young I was). Since that very early lesson, I’ve learned how to spell roux, and how to adjust it for different applications.

The intensity of cooking on the roux changes its properties, and you can easily use this to your advantage, based on what you are making. For a thick, creamy white sauce, cook the flour in the butter over medium heat, just long enough to achieve a foamy appearance, then add milk all at once and whisk until it is thickened. Season it with salt and pepper, perhaps a little grated nutmeg (essential, in my opinion, for a real bechamel) or another seasoning you like, to match how you plan to use it. If I were to layer this creamy sauce with thinly sliced Yukon gold potatoes and onions, I might substitute ground cumin for the nutmeg, because I love the flavor of cumin with potatoes. Slide that into the oven for about an hour, and you’d be enjoying scalloped potatoes. Melt cheese into the sauce before layering, and you’d have potatoes au gratin.

Cook the flour and butter a bit longer to the point of being brown and toasty-looking, and you’ll have a roux with more complex flavor, but slightly less thickening power. This is what I usually do when I make mac and cheese, because I don’t need the bechamel to be quite as thick on its own (the melted-in cheese makes up for that), and because the browned butter in the base lends a warm, nutty aroma and flavor to the dish.

Incidentally, it does not have to be real butter. A roux can be made with any type of fat, including plant-based butters, cooking oil or even lard or bacon grease. I have also found success using gluten-free flour, as there is usually enough starch in it to produce similar results as one made with regular, all-purpose flour. I have even read that almond flour can be used in roux (though I have not tested this). As long as the starch and fat molecules play nice, you’ll end up with a roux that will thicken. 

For a roux with even more heft and complexity, such as for gumbo, cook the flour in oil rather than butter, and do it low and slow—even in the oven, if you want to go hands-free—and you’ll have a developed flavor that can’t be equaled with any add-in ingredient. More on that another day. 😊

The dish I’m sharing today is another spin on my basic mac and cheese, with the addition of chipotle, one of the most favored flavors at our house. Though a subtle touch of chipotle could be added with a few sprinkles of ground chipotle powder (either before or after the cheese is added to the roux), I’ve opted to use a couple of spoonsful of pureed chipotle with adobo sauce. These are the little cans you find in the “international” section of the supermarket. Chipotle peppers are essentially dried, smoked jalapenos that have been rehydrated to a plump state. We dump the entire contents of a small can into the food processor, to be used in a variety of Mexican-themed dishes, including Les’s Smoky Guacamole and my South of the Border Crab Cakes.

For this batch of mac and cheese, I chose whole grain rotini because of its heft and texture. When you choose a pasta with lots of surface area, you should expect to adjust the pasta-to-sauce ratio (all those twists and curves are going to need extra sauce). I topped the dish with a mixture of crushed crispy fried jalapenos (from Trader Joe’s) and plain panko breadcrumbs.

As for the cheese, I went with a medium-sharp cheddar as the main flavor, but the base cheese is yellow American. You probably already know that very sharp cheeses do not melt as well as their milder counterparts. And I’m sure you know about the exquisite melting qualities of American cheese, despite its bad rap, which is not fairly earned.

Saying “American cheese is not cheese” is like saying “meatloaf is not meat.”

J. Kenji Lopez-Alt


2 Tbsp. extra virgin olive oil

1/2 large onion, diced fairly fine

3 Tbsp. salted butter

4 Tbsp. all-purpose flour

2 cups milk

6 oz. yellow American cheese, cubed* (see notes)

10 oz. medium-sharp yellow cheddar, shredded

2 Tbsp. chipotle w/ adobo puree (more or less, depending on your tolerance for heat)

A few shakes of ground cumin, for added smokiness

Salt and pepper to taste

2/3 lb. whole grain rotini (if using smoother pasta, use an entire pound)


1/3 cup crispy fried jalapenos (or fried onions, if you prefer less heat)

1/4 cup plain panko breadcrumbs


I used to think that American cheese was fake food, but this article on Serious Eats convinced me otherwise. Yes, it is processed, but it is not made up of ingredients and chemicals pretending to be cheese. It is real cheese, processed with special salts to result in a smooth, creamy texture when melted. I do not feel this way about the brand that begins with a V (and I think you all know which one I’m referring to), but I am OK with American cheese now and then, and I consider it essential as a melting base for my mac and cheese. Yeah, what J. Kenji said.

If you have an immersion blender, I encourage you to take the step I’ll describe for whipping your cheese sauce into ultra-creamy territory. It is optional, of course, but a total game changer in my mac and cheese endeavors.


Smoky Chipotle Mac & Cheese!

4 thoughts on “Smoky Chipotle Mac & Cheese

  1. Pingback: Smoky Chipotle Mac & Cheese — Comfort du Jour | My Meals are on Wheels

  2. Such a wonderful blank slate, and the chipotle sounds perfect! My own personal favorite is lobster mac and cheese, and since we have to be really careful about dairy, I only make it now on holiday gatherings, like Easter! The kids always request my homemade mac and cheese on the menu, so I make it, regardless of what else I’m serving!

    Liked by 1 person

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