Ultimate Creamy Chipotle Mac and Cheese: A Smoky & Spicy Homemade Comfort Food Recipe
Macaroni and cheese holds a special place in our hearts as the quintessential comfort food. But imagine elevating this classic to new heights with a touch of smoky spice. This Chipotle in Adobo Macaroni and Cheese recipe delivers just that: a luxuriously creamy, perfectly spicy, and wonderfully smoky dish that will become an instant favorite. Topped with a golden, buttery, and aromatic Ancho Chile Panko crust, it transforms from a simple side into an unforgettable culinary experience.
There are countless ways to prepare macaroni and cheese, but our deep affection for chipotles in adobo shines through in this particular creation. You’ll often find these versatile peppers featured in many of our recipes, and for good reason. They impart a distinct, rich smoky flavor without overwhelming the palate with excessive heat. The spice level is just right, offering a pleasant warmth that perfectly complements the creamy cheese sauce, making every bite a delight.

We’ve meticulously crafted this homemade mac and cheese recipe using a blend of cheeses that are readily available at most grocery stores, ensuring accessibility without compromising on flavor or quality. For those looking to further enhance their creamy mac and cheese experience, we’ve included additional suggestions at the bottom of this post to help you truly master this dish and impress your family and friends. Get ready to dive into the world of rich, smoky, and spicy comfort!
How to Make Chipotle in Adobo Macaroni and Cheese from Scratch
The secret to a truly outstanding creamy macaroni and cheese sauce often begins with a well-made roux. If this is your first time venturing into roux-making, don’t be intimidated! It’s a fundamental cooking technique that involves simply combining equal parts butter and flour, cooked together to form a thickener. This golden paste is crucial for binding the cheeses into a smooth, velvety sauce that will lovingly cling to every piece of macaroni, ensuring a consistently creamy texture throughout the dish.
Admittedly, perfecting a roux and a cheese sauce has taken me years of practice, but now it feels like second nature. It’s one of those culinary skills that, once mastered, opens up a world of possibilities. I remember my mom making a stovetop Mexican-inspired mac and cheese when we were kids. It featured macaroni, Monterey Jack cheese, tomato sauce, and minced onions, boasting an incredible cheese pull that we absolutely loved. Interestingly, she only made that version when we were young; nowadays, she prefers a more classic roux-based sauce, much like the one we’re making today. Her current method showcases how a simple roux provides a stable and delicious foundation for endless cheese sauce variations.
Choosing the Perfect Cheeses for Your Smoky Mac and Cheese
A crucial note about the cheeses: for the best flavor and melt, it is highly recommended to shred your own cheese just before preparing this spicy mac and cheese recipe. While pre-shredded cheese offers convenience, freshly shredded cheese melts more smoothly and releases significantly more flavor into your sauce, creating a richer and more aromatic result. The difference is truly noticeable and worth the extra step.
For this Chipotle Mac and Cheese, we use a delightful trio: Colby Jack, Mozzarella, and Extra Sharp Cheddar. Colby Jack provides a mild, creamy base with good melting properties. Mozzarella adds an extra layer of stretchiness and mildness, contributing to that irresistible “cheese pull” factor. Finally, the extra sharp cheddar delivers a robust, tangy flavor that cuts through the creaminess and stands up well to the smoky chipotle. This combination ensures a complex yet balanced flavor profile and a perfectly smooth, decadent texture for your Adobo macaroni and cheese.
For a step-by-step guide to making this delicious Chipotle in Adobo Macaroni and Cheese, refer to the complete recipe card below. Here’s a quick overview of the essential cooking steps:
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How to Make the Roux for a Creamy Sauce
Begin by melting butter in a large skillet or a 3-quart saucepan over medium heat. Once the butter has completely melted and is slightly foamy, add the all-purpose flour. Whisk continuously until the butter and flour are fully combined and form a smooth paste. Continue to whisk this roux for 1-2 minutes until it becomes bubbly, light golden, and develops a slightly nutty aroma. This cooking time helps remove the raw flour taste.
Gradually pour in the cold milk while constantly whisking to ensure the flour is completely incorporated and no lumps form. Season the mixture with 1/2 tsp of salt and 1/2 tsp of pepper. Continue to cook the roux for about 3 minutes, stirring constantly to prevent burning, especially at the bottom of the pan. The mixture should thicken significantly, and you should see gentle bubbles forming on the surface, indicating it’s ready for the cheese.
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Crafting the Rich Chipotle Cheese Sauce
Reduce the heat to low. Add the shredded Colby Jack cheese, extra sharp cheddar, and Mozzarella to the thickened roux. Continue to whisk gently and consistently until all the cheese is completely melted and the sauce achieves a uniform, creamy consistency. This process typically takes about 5 minutes, ensuring a perfectly smooth and lump-free cheese sauce.
Next, incorporate the finely minced Chipotle peppers in adobo, along with some of their flavorful liquid. Stir thoroughly until the smoky, spicy chipotle is fully combined and evenly distributed throughout the rich cheese sauce, infusing it with its signature flavor. Taste and adjust seasoning if necessary, keeping in mind the heat will intensify slightly upon baking.
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Assembling and Baking Your Comforting Casserole
Preheat your oven to 350°F (175°C). Add the cooked and well-drained macaroni (or your pasta of choice, such as cavatappi) to a buttered, oven-safe casserole dish. Pour the prepared Chipotle cheese sauce over the macaroni. Gently stir the pasta and sauce until every piece of macaroni is thoroughly coated in the rich, creamy sauce, ensuring a consistent flavor in every bite.
For an extra layer of flavor and crunch, sprinkle grated Parmesan cheese over the macaroni and cheese. Then, evenly spread the buttered Ancho Chile Panko breadcrumbs (prepared as per the recipe card) over the top. Bake the casserole for 20-25 minutes, or until the topping is golden brown and crispy, and the cheese sauce is bubbly around the edges. Allow it to rest for a few minutes before serving to ensure the sauce sets beautifully.






How to Elevate Your Chipotle in Adobo Macaroni and Cheese Recipe
While this Chipotle in Adobo Macaroni and Cheese recipe is already a star on its own, cherished for its unique flavor, delightful texture, and zesty kick, there are several ways to take it to legendary “superstar hero” status. Looking to impress? Here’s how you can truly step up your gourmet mac and cheese game:
- Smoked Cheese Upgrade: For an even deeper smoky profile, consider substituting one cup of the Colby Jack cheese with a high-quality smoked cheese. My personal favorite is an Apple Smoked Gruyere, often found at specialty stores like Sprouts. Its nutty, smoky notes complement the chipotle beautifully, adding another layer of complexity. Other excellent choices include smoked gouda or smoked cheddar.
- Protein Power-Up: Transform this side dish into a complete meal by topping it with some fantastic protein. Think tender pulled pork mac and cheese, succulent sautéed shrimp, or crispy bacon bits. These additions not only add substance but also introduce new textures and flavors that harmonize wonderfully with the spicy cheese sauce.
- The Ultimate Indulgence: For a truly extravagant experience, crown your mac and cheese with glorious lobster! Lobster meat adds a sweet, delicate flavor that contrasts beautifully with the smoky heat, making it an extraordinary dish for special occasions.
- Creamy (No Bake) Version: If you prefer an ultra-creamy, almost soup-like consistency, you can omit the Ancho Chile Panko topping and serve this stovetop chipotle mac and cheese straight from the pot. It’s perfect for those who crave maximum lusciousness without the baked crust.
- Herbaceous Freshness: A sprinkle of fresh chopped cilantro or parsley just before serving can add a pop of color and a refreshing counterpoint to the rich flavors.
- Spicier Kick: If you’re a true heat seeker, you can increase the amount of chipotle in adobo or add a pinch of cayenne pepper to the cheese sauce. Be mindful, as chipotles can vary in heat!
These simple adjustments can turn an already amazing dish into a personalized masterpiece, perfectly suited to your taste and occasion. Enjoy experimenting and finding your favorite variation of this spicy comfort food!

Inspired by this recipe? We would love to see your creations! Make sure to mention us or tag us on Instagram when you share your delicious Chipotle Mac and Cheese. All content and photographs ©Claudia’s Table and claudiastable.com.

Chipotle in Adobo Macaroni and Cheese
Ana | Claudia’s Table
February 17, 2021
Pin Recipe
20 minutes
25 minutes
45 minutes
Barbeque, Side Dish
American
8
530
kcal
Equipment
-
large skillet or 3 qt sauce pan
-
oven safe casserole dish
Ingredients
-
1
lb
pasta
Cavatappi or elbow -
2
cups
Colby Jack cheese
shredded -
1
cup
Mozzarella cheese
shredded -
1
cup
Extra sharp cheddar cheese
shredded -
3-4
whole
Chipotles in Adobo
finely chopped with liquid -
1/2
cup
Panko
Japanese breadcrumbs -
1/2
cup
parmesan
grated -
3
tbsp
flour
all purpose -
4
tbsp
butter
3 tbsp for roux + 1 tbsp for panko -
1/2
tsp
Ancho chile powder -
2 3/4
cup
milk
whole, cold -
1/2
tsp
salt -
1/2
tsp
pepper
Prevent your screen from going dark
Instructions
-
Preheat oven to 350 degrees F (175 C).
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Cook macaroni/pasta according to package directions until al dente. Drain well.
-
Melt 3 tablespoons of butter in a large skillet or 3 qt sauce pan over medium heat. Once butter is melted and slightly foamy, add the flour and whisk constantly until fully combined. Continue to whisk the roux for 1-2 minutes until it becomes bubbly and light golden brown, developing a nutty aroma.
-
Gradually add the cold milk to the roux while continuously whisking to ensure no lumps form and the flour is completely incorporated. Add 1/2 tsp of salt and 1/2 tsp of pepper. Cook the roux for about 3 minutes, continuing to whisk so it doesn’t burn on the bottom. The mixture should thicken considerably and show gentle bubbles on the surface.
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Reduce heat to low. Add the Colby Jack, Mozzarella, and extra sharp cheddar cheeses to the roux and stir until the cheese is fully melted and the sauce is smooth and creamy. Continue stirring for about 5 minutes until the sauce is completely combined and thickens slightly to a pourable consistency. Add the finely chopped chipotle chiles and their adobo liquid to the cheese mixture and stir until fully combined.
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Place the well-drained, cooked macaroni/pasta in a buttered oven-safe casserole dish. Pour the rich chipotle cheese sauce over the pasta.
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Stir gently until all the macaroni/pasta is fully and evenly covered in the luscious cheese sauce.
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Evenly sprinkle the grated Parmesan cheese on top of the macaroni and cheese.
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In a small pan, melt the remaining 1 tablespoon of butter over medium-low heat. Once melted, add the Panko breadcrumbs and stir continuously until they are completely covered in butter and toasted to a light golden brown. Sprinkle in the Ancho Chile powder and mix well to combine.
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Evenly spread the buttered Ancho Chile Panko breadcrumbs over the top of the casserole.
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Bake for 20-25 minutes, or until the topping is golden brown and crispy, and the cheese sauce is bubbly and heated through. Let stand for a few minutes before serving.
Notes
Nutrition
Serving:
1
cup
Calories:
530
kcal
Nutritional information is calculated online and should be used as a guide.
baked macaroni and cheese, chipotle, macaroni and cheese, spicy mac and cheese, homemade mac and cheese, comfort food
All content and photographs ©Claudia’s Table and claudiastable.com
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Frequently Asked Questions About Chipotle Mac and Cheese
While our recipe features a fantastic blend of Colby Jack, Mozzarella, and Extra Sharp Cheddar, you certainly have room for experimentation. You can easily swap Mozzarella and Colby Jack for a full three cups of straight cheddar cheese if you prefer. However, we highly recommend incorporating at least one cup of extra sharp cheddar for its robust flavor, or even a smoked cheddar or Gruyere to introduce a deeper, more sophisticated note that complements the chipotle beautifully. Feel free to play with your favorite melting cheeses!
Absolutely! The Ancho Chile powder adds an extra layer of earthy, mild heat and a beautiful reddish hue to the Panko topping, enhancing the overall flavor profile of the spicy mac and cheese. However, if you prefer a less complex flavor, or simply don’t have it on hand, you can definitely omit it. Just follow the recipe instructions for preparing the buttered Panko without adding the powdered chile. The topping will still provide a delightful crunch!
Yes, you absolutely can use gluten-free pasta! Typically, gluten-free pasta packages come in 12 oz (340g) quantities, slightly less than regular pasta. However, you can still make the same amount of cheese sauce as specified for 16 oz of regular pasta. Gluten-free pasta tends to absorb liquid more readily, so the final consistency of your baked dish will be similar to using regular pasta, especially after it has absorbed some of the creamy sauce during baking. Just follow the package directions for cooking the gluten-free pasta until al dente before mixing with the sauce.
While we highly recommend using canned chipotles in adobo sauce for their superior flavor and texture in this recipe, if they are genuinely unavailable, you can substitute with chipotle pepper powder. For each whole chipotle en adobo specified in the recipe, an equivalent powder measurement is approximately 1 teaspoon. However, please be aware that the taste of the canned chipotles, with their smoky, sweet, and slightly tangy adobo sauce, is far superior and adds a depth of flavor that is difficult to replicate with just powder. Seek out the canned version if at all possible!
Leftover chipotles in adobo are a culinary gem and can be easily stored for future use. One popular method is to freeze the chiles; however, fair warning: freezing can intensify their heat, making them surprisingly spicy once thawed. Alternatively, they can be kept in the refrigerator for 1-2 months in a tightly sealed container. We prefer using a glass container for storage, as it doesn’t seem to intensify the heat as much as freezing. For more detailed tips on storing canned leftovers, check out our comprehensive post on How to Store Canned Leftovers. Don’t let those delicious peppers go to waste!