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Spicy Jalapeno Baked Macaroni and Cheese

Cooking Laboratory

November 23, 2020 | Updated July 29, 2022 | Laura

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This is hands-down my favorite mac and cheese recipe. It's so creamy, so cheesy, and just the right amount of spicy that it has me craving it all year long! This baked macaroni and cheese recipe is made with both cheddar cheese and pepper jack cheese, and the jalapenos bring in some heat. It definitely earns a spot as a side dish on your Thanksgiving table. You're sure to love this homemade mac & cheese as it is the ultimate comfort food!

Spicy Jalapeno Baked Macaroni and Cheese

Sharp cheddar cheese, pepper jack cheese, jalapenos, onions, garlic, butter, and pasta... How could it be bad?

Are you one of those people that gets a little bit disappointed when you don't see macaroni and cheese sitting on the Thanksgiving table? If so, you're in the right place.

In order to honor one of the best holidays [Thanksgiving] and one of the best side dishes [macaroni and cheese], I have dedicated my third Cooking Laboratory video to Baked Macaroni and Cheese.

I know 2020 Thanksgiving will be different, but hopefully this delicious spicy cheesy pasta will boost your mood.

I'm usually all for keeping traditional recipes traditional, but I couldn't help myself from adding in some heat into this creamy baked mac & cheese.

I skipped the garlic and onion powder and went for throwing in real onion and garlic right into the pasta. I added in minced jalapenos with all of their seeds for maximum spicy! The canned cream of condensed soup made this macaroni and cheese the creamiest without covering up the delicious extra-sharp cheddar cheese flavor. I also added pepper jack cheese to contribute to the creaminess and add little more kick.

You better believe that this will be served at Thanksgiving at our house even if it's just the two of us. We could all use a little (or lot- I'm not judging) comfort food during the 2020 holidays!

Cooking Laboratory

How did I come up with this recipe? Well, I looked into the history of mac & cheese, learned about pasta science, and made four other baked macaroni and cheese recipes that I found online. I then took what I learned in my lab (AKA: my kitchen), and through trial & error came up with this wonderful baked macaroni and cheese with a kick.

✽ If you are interested the history of macaroni and cheese, pasta science, and watching the taste tests- click the video below!

Let’s talk about the other four recipes that I chose to make!

Baked Macaroni and Cheese Recipes

Baked Macaroni and Cheese Recipes

First, I made Mom on Timeout's Best Homemade Baked Mac and Cheese (Mom on Timeout Homepage).

This baked macaroni and cheese was oh so creamy from using heavy cream instead of milk. The cheeses used were sharp cheddar and gruyere. The gruyere stole the show and makes such a lovely cheesy pasta. The Panko bread crumbs and Parmesan topping added the perfect amount of crunch.

Baked Macaroni and Cheese Recipes

Second, I made Dinner then Dessert's Baked Mac and Cheese (Dinner then Dessert Homepage).

I loved flavors of the added mustard powder, cayenne pepper, and paprika. The addition of a large egg helped make the pasta creamy which was nice. The cheeses were Monterey Jack, Mozzarella, and Sharp Cheddar. The use of three different cheeses gives a deep flavor to the mac & cheese which I enjoyed.

Baked Macaroni and Cheese Recipes

Third, I made Immaculate Bite's Southern Baked Mac and Cheese (Immaculate Bites Homepage).

The use of evaporated milk in this recipe resulted in a smooth cheese sauce due to the high amount of milk proteins. This recipe does not skimp on the spices. It calls for onion powder, garlic powder, creole seasoning, and cayenne pepper. The cheeses used were Jack, Mozzarella, and Sharp Cheddar. Again, this combination of cheeses makes for a really good pasta!

Baked Macaroni and Cheese Recipes

Lastly, I made Spend with Pennies' Homemade Mac and Cheese Casserole (Spend with Pennies Homepage).

This recipe had such a creamy cheese sauce from the addition of canned condensed cheddar soup. It was a great consistency! The addition of mustard powder and onion powder brought in some flavor. The cheeses used were sharp cheddar and parmesan. Of course, you can never go wrong with a cheddar mac and cheese.

The Winner

All of these recipes were so good. I highly recommend you try them out! After a randomization and a blind taste test, my husband chose (drum roll please) Spend with Pennies' Homemade Mac and Cheese Casserole as his favorite. He loved how creamy this mac and cheese was and the perfect consistency of the sauce. That's my type of pasta!

My Delicious Spicy Macaroni & Cheese Recipe

Jalapeno Mac and Cheese

✽ Pasta

I explain the details of why I chose not to boil my pasta in my cooking laboratory video. I got the idea from The Food Lab

Basically, the option of soaking the noodles for 30-45 minutes prior to adding them to the casserole dish allowed the pasta to have the perfect texture. The noodles absorbed all the water, but we didn't have to sacrifice the starch leaving us a perfectly al dente noodle that won't steal all of the liquid from our sauce.

It's a very simple process. Instead of boiling the noodles, cover them with hot salt water for 30-45 minutes. This is the perfect time to prep the rest of the recipe!

✽ Liquids

I personally liked the flavors and consistency of just plain whole milk for the sauce. I substituted some whole milk for half & half to add little more creaminess to the pasta.

✽ Vegetables

I knew that I wanted my macaroni and cheese recipe to be spicy. I love spicy food and jalapeños, and they work well with cheddar cheese so that's what I chose. Spicy cheese sauce? Yes, please! Since I was already going to be sautéing the fresh jalapeños in the butter, I went ahead and threw in onion and garlic too instead of using onion and garlic powder.

✽ Cheese

I chose extra-sharp cheddar cheese because I love the flavor of it and it takes the flavor of this pasta to the next level. It's also a great cheese to use in macaroni and cheese given its relatively low melting point. In addition, I also threw in some pepper jack. Monterey Jack cheese is great to use in macaroni and cheese as well because it adds creaminess to the sauce. I decided to go with pepper jack for a little extra kick. The condensed cheddar cheese soup is the key to getting a really creamy sauce.

✽ Seasonings

I went with the classic macaroni and cheese seasonings: mustard powder, cayenne pepper, and paprika. I also added in a little bit of hot sauce to give this mac & cheese just the right amount of spice.

Homemade Mac and Cheese

✽ Topping

I believe baked mac and cheese needs that crunch so I decided to top my pasta with a breadcrumb topping. Instead of using store bought breadcrumbs which can have the tendency of getting mushy and tasting stale, I opted for making my own with white bread. I threw the bread in the food processor along with some butter, onion powder, and parmesan. The crunchy cooked parmesan on top really makes this mac and cheese a winner.

Spicy Mac & Cheese Recipe Video

For this recipe:

*Some of these ingredient links may be affiliate links. As an Amazon Associate I earn from qualifying purchases.*

Cooking Laboratory Baked Spicy Jalapeno Mac and Cheese

Spicy Jalapeno Baked Mac & Cheese

By Laura | Laura the Gastronaut
Soak Time: 45 minutes | Prep Time: 10 minutes | Cook Time: 1 hour 20 minutes | Total Time: 2 hours 15 minutes
Yield: one 9x13 baking dish, serves 10


This is hands-down my favorite mac and cheese recipe. It's so creamy, so cheesy, and just the right amount of spicy that it has me craving it all year long! This baked macaroni and cheese recipe is made with both cheddar cheese and pepper jack cheese, and the jalapenos bring in some heat. It definitely earns a spot on your Thanksgiving table. You're sure to love this homemade mac & cheese as it is classic comfort food!

*Some of these ingredient links may be affiliate links. As an Amazon Associate I earn from qualifying purchases.*

**Read entire recipe and the notes down below the recipe prior to cooking for best results.**


• 16 oz elbow macaroni pasta
Kosher salt
• 7 1/2 tablespoons butter, divided
• 2 slices white bread, crusts cut off & torn into large pieces
• 1/2 cup (2 oz) fresh Parmesan cheese, grated
• 1/2 teaspoon onion powder
• 1/2 cup onion, minced
• 4 jalapenos, 3 minced with seeds kept in and one thinly sliced for topping
• 2 garlic cloves, minced
• 1/4 cup (34 grams) all-purpose flour
• 1 cup (237 mL) half & half
• 2 cups (473 mL) whole milk
• 1 teaspoon hot sauce
• 1 teaspoon dry mustard powder
• 1 teaspoon paprika
• 1/4 teaspoon cayenne pepper
• 1/4 teaspoon ground black pepper
• 2 1/2 cups (10 oz) sharp cheddar cheese, grated
• 2 1/2 cups (10 oz) pepper jack cheese, grated
• 1 can (10 1/2 oz) canned condensed cheddar cheese soup


Soak the pasta: In a large bowl, cover the pasta with hot salted water for 30-45 minutes. Stir after 5 minutes to prevent sticking. Drain.
Prepare Topping: Cut 1 1/2 tablespoons butter into smaller pieces. In a food processor, blend together white bread, Parmesan cheese, onion powder, and the 1 1/2 tablespoons of butter until well combined- about 10-15 pulses. Set aside.
Preheat oven to 375°F.
Make Sauce: Melt 6 tablespoons of butter in a large heavy-bottomed pot over medium-high heat. Add in minced onion and 3 minced jalapenos to the melted butter. Cook for 2-3 minutes until fragrant. Add in garlic and cook for an additional 30 seconds.
⑤ Whisk in flour and continue whisking constantly for 1-2 minutes until the flour is a light golden color and fragrant.
⑥ Very slowly pour in half & half followed by the whole milk whisking the entire time. Keep whisking until the mixture is boiling.
⑦ Once it begins to boil, reduce heat to medium-low. Stir in hot sauce, mustard powder, paprika, cayenne powder, and black pepper and simmer for 5 minutes. Whisk often to ensure the sauce is not burning on the bottom.
⑧ Once the sauce is thickened, add in half of the grated cheddar and pepper jack cheese. Stir until melted, and then stir in the other half of the grated cheeses until melted.
⑨ Stir in condensed cheddar cheese soup until fully incorporated.
⑩ Stir in drained soaked elbow pasta until everything is mixed together and all of the pasta is coated in the cheesy sauce.
Pour the mixture into a greased 9 x 13 casserole dish. Cover the top of the pasta with the breadcrumb mixture. Place jalapeno slices on top.
Bake: Cover the dish with foil and bake on the middle rack for 45 minutes. Remove foil and bake for an additional 15 minutes or until the mac and cheese is golden brown on top.


Soaking Pasta: For the hot water, I just use hot tap water. Put a lot of salt into the water- enough so it tastes like the ocean!
Breadcrumbs: You can use store bought breadcrumbs if you need to, but you will be losing crispiness and crunch. Fresh breadcrumbs also provide better flavor!
Vegetables: If you don't have fresh onion or garlic, that's okay. You could add 1 teaspoon of garlic powder and 1 teaspoon of onion powder instead when you add the other seasonings into the sauce.
Jalapenos: I love jalapeno flavor, and I like things spicy so I go all in with 3 big jalapenos with their seeds in the sauce and 1 sliced jalapeno on top. If you don't want that much jalapeno, you can adjust the spice level by just adding in 1, 2, or 3 of them. You can also not add in all the seeds if you don't want it to get too spicy.
Making Roux: It's so important to whisk constantly after adding in the flour to break up clumps and prevent burning. When you add in the milk, make sure to add slowly while you are whisking. It should take you 15-30 seconds to add in all the milk and half & half. Keep a close eye on the sauce and whisk often while it simmers so you don't scorch the bottom!
Adding in Cheese: I mix the two cheese together and add in half at a time. If too much cheese is added at one time the sauce can split or become unstable. Adding in small amounts will prevent the grease in the cheese from separating out.
Condensed Cheddar Cheese Soup:I highly recommend you add this into the sauce. This is going to make the pasta so creamy and delicious. If you do not have condensed cheddar soup on hand, you should check out the other recipes I made above that do not call for this ingredient!


✽ Did you make this recipe?
Let me know by leaving a comment below and sharing on Instagram. Tag @laurathegastronaut and hashtag it #laurathegastronaut.

Category: Sides, Thanksgiving, Vegetarian Cuisine: American
Keywords: jalapeno baked mac and cheese, spicy baked mac and cheese, spicy homemade mac and cheese, southern jalapeño mac and cheese, spicy classic mac and cheese

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More Pasta Recipes:

Homemade Pumpkin Pasta with Pumpkin Sauce (another great fall recipe that is the perfect comfort food)
Burst Tomato and Basil Pasta with Salami (this pasta is so delicious and so simple to make)
→ Check out all of my dinner recipes!

Bon appétit!

November 23, 2020 by Laura Bullock

*This Spicy Jalapeno Baked Macaroni and Cheese blog post and recipe may contain some Amazon affiliate links. These link to products that I personally use and recommend. If you purchase anything using my links, it will not cost you anything. It will though give some financial support which helps me keep this blog running. Thank you for reading my blogs and your continued support.