Queso Mac & Cheese with Chipotle and Fresh Toppings Recipe
Introduction
This Queso Mac & Cheese is a creamy, cheesy twist on the classic comfort dish, with a smoky chipotle kick for added depth. Perfect for those who love bold flavors in a rich, melty pasta bake.

Ingredients
- 1/2 cup unsalted butter, plus more for pan
- Kosher salt
- 1 lb cavatappi, elbow, or other short, tube-shaped pasta
- 1/2 cup all-purpose flour
- 8 oz cream cheese, room temperature
- 1 canned chipotle chile, finely chopped (optional), plus 2 to 4 oz adobo sauce (depending on heat preference)
- 1 tsp ground cumin
- Freshly ground black pepper
- 12 oz sharp cheddar cheese, coarsely grated
- 12 oz Monterey Jack cheese, coarsely grated
- Sliced avocado, pickled jalapeños, and chopped fresh cilantro, for serving
Instructions
- Step 1: Preheat the oven to 425°F. Grease a 13″ x 9″ baking pan or two 8″ x 5″ casserole dishes with butter.
- Step 2: Bring a large pot of salted water to a boil. Cook the pasta, stirring occasionally, until it is slightly firmer than al dente—about 2 minutes less than the package directions. Reserve 4 cups of the pasta water, then drain the pasta. If you don’t have enough reserved pasta water, add water or milk to reach 4 cups total liquid.
- Step 3: In the same pot, melt the butter over medium heat. Whisk in the flour and cook, whisking constantly, until the butter foams and turns golden brown, about 4 minutes. Slowly whisk in the reserved pasta water to avoid lumps. Add the cream cheese and whisk until the sauce is smooth.
- Step 4: Stir in the chipotle chile and adobo sauce (if using) and the cumin. Season with salt and freshly ground black pepper. Bring the sauce to a simmer while whisking constantly. Gradually add the cheddar and Monterey Jack cheeses in 1/2 cup increments, whisking until melted and smooth before adding more. Add the cooked pasta, season with salt and pepper, and toss to combine. Transfer the mixture to the prepared baking pan.
- Step 5: Place the pan on a foil-lined baking sheet and cover it with foil. Bake for 30 minutes, then remove the foil and continue baking until the cheese bubbles, about 10 minutes more. Top with sliced avocado, pickled jalapeños, and chopped fresh cilantro before serving.
Tips & Variations
- For a milder dish, omit the chipotle chile and adobo sauce or reduce the amount used.
- Use a mix of cheeses like mozzarella or pepper jack for different flavor profiles.
- Add cooked bacon or grilled chicken for extra protein.
- If you prefer a crispier top, sprinkle extra cheese or breadcrumbs before the final bake.
Storage
Store leftover mac and cheese in an airtight container in the refrigerator for up to 3 days. Reheat gently in the oven or microwave, adding a splash of milk or water to loosen the sauce if needed.
How to Serve

Serve this delicious recipe with your favorite sides.
FAQs
Can I make this recipe without cream cheese?
Cream cheese adds creaminess and richness, but you can substitute it with extra sharp cheddar or a bit of sour cream for a slightly different texture and flavor.
How spicy is the chipotle adobo sauce?
The chipotle and adobo sauce provide a smoky heat that can be quite spicy; adjust the amount based on your heat preference or omit it entirely for a milder version.
PrintQueso Mac & Cheese with Chipotle and Fresh Toppings Recipe
This Queso Mac & Cheese recipe offers a rich, creamy twist on the classic comfort food with a blend of sharp cheddar and Monterey Jack cheeses, complemented by a smoky chipotle kick. Perfectly baked to achieve a bubbly golden crust and topped with fresh avocado, pickled jalapeños, and cilantro for added zest and freshness.
- Prep Time: 15 minutes
- Cook Time: 40 minutes
- Total Time: 55 minutes
- Yield: 8 servings 1x
- Category: Main Dish
- Method: Baking
- Cuisine: American
Ingredients
Pasta and Butter
- 1/2 cup unsalted butter, plus more for pan greasing
- Kosher salt, to taste
- 1 lb cavatappi, elbow, or other short, tube-shaped pasta
Sauce
- 1/2 cup all-purpose flour
- 8 oz cream cheese, room temperature
- 1 canned chipotle chile, finely chopped (optional)
- 2 to 4 oz adobo sauce (depending on heat preference)
- 1 tsp ground cumin
- Freshly ground black pepper, to taste
- 12 oz sharp cheddar cheese, coarsely grated
- 12 oz Monterey Jack cheese, coarsely grated
Toppings
- Sliced avocado, for serving
- Pickled jalapeños, for serving
- Chopped fresh cilantro, for serving
Instructions
- Prepare Oven and Pan: Preheat your oven to 425°F (220°C). Grease a 13″ x 9″ baking pan or two smaller casserole dishes (8″ x 5″) with butter to prevent sticking and ensure an easy release after baking.
- Cook Pasta: Bring a large pot of salted water to a boil. Cook the pasta according to package instructions but reduce the cooking time by about 2 minutes, so it is slightly firmer than al dente. Stir occasionally to prevent sticking. Before draining, reserve 4 cups of the pasta cooking water. If not enough liquid remains, supplement with water or milk. Drain the pasta and set aside.
- Make Roux and Cheese Sauce: Using the same pot, melt 1/2 cup butter over medium heat. Whisk in the flour and cook, whisking constantly for about 4 minutes until the roux foams and turns golden brown. Gradually whisk in the reserved pasta water slowly to avoid lumps. Add the cream cheese and whisk until fully melted and smooth.
- Add Flavorings and Cheese: Stir in the finely chopped chipotle chile (if using), adobo sauce, ground cumin, salt, and freshly ground black pepper. Bring the mixture to a simmer, whisking constantly. Add the cheeses a half-cup at a time, whisking after each addition until smooth and melted. Once the sauce is ready, fold in the cooked pasta, adjust seasoning with salt and pepper, and toss to combine thoroughly.
- Assemble and Bake: Transfer the cheesy pasta mixture to the prepared buttered baking dish. Place the dish on a foil-lined baking sheet and cover with foil. Bake in the preheated oven for 30 minutes. Remove the foil and continue to bake until the cheese is bubbly and slightly browned on top, approximately 10 more minutes.
- Garnish and Serve: Remove the baked mac & cheese from the oven and top with sliced avocado, pickled jalapeños, and chopped fresh cilantro. Serve warm and enjoy your creamy, smoky queso mac & cheese!
Notes
- Cooking pasta slightly firmer than al dente ensures it doesn’t become mushy after baking.
- Adjust chipotle and adobo sauce quantities to control the heat level of the dish.
- Using a mix of sharp cheddar and Monterey Jack provides a balanced sharp and creamy flavor.
- Covering the pan with foil during the initial bake prevents the top from drying out before the pasta is heated through.
- Foil-lined baking sheet helps catch any overflowing cheese sauce, making cleanup easier.
- For a gluten-free version, use gluten-free pasta and flour substitutes.
Keywords: Queso Mac and Cheese, Cheesy Pasta Bake, Baked Mac and Cheese, Chipotle Mac and Cheese, Creamy Mac and Cheese

