Homemade Three Cheese Macaroni and Cheese (Best Baked Mac and Cheese)

Published: Nov 20, 2025 · Modified: Jan 17, 2026 by Eileen Murphy Kelly

Our Three Cheese Mac & Cheese is the ultimate comfort food meal. This made-from-scratch cheesy pasta casserole is a luscious mix of melting cheeses. The combination of the bold flavors of sharp cheddar cheese, the stretch melty mozzarella cheese adds to the sauce, and Colby Jack gives it a rich and creamy sauce. Whether it’s a weeknight dinner or a holiday side, this baked mac and cheese recipe with three cheeses delivers a velvety sauce and irresistible cheese pull every time.

A white casserole dish with homemade macaroni and cheese. A wooden spoon picking up some of the mac and cheese.

For specific details on the recipe, use the table of contents to click on sections of the recipe.

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Why You Will Love Three Cheese Macaroni and Cheese
Ingredients you Need for 3 Cheese Mac and Cheese
Equipment needed for Homemade Macaroni and Cheese
How to make Three Cheese Macaroni and Cheese
Make-ahead, storage, and freezer tips
Eileen's Tips for the Best Macaroni and Cheese
Homemade Mac and Cheese Recipe - Tips and Variations
Best Cheese Combos for the Cheesiest Macaroni and Cheese
FAQs for the Best Three Cheese Macaroni and Cheese
What to serve with Three Cheese Macaroni and Cheese
More Easy Pasta Recipes
📖 Recipe
💬 Comments

Why You Will Love Three Cheese Macaroni and Cheese

Cheese Sauce: The melting factors of the three cheese types we chose create the perfect blend of cheese that melts into gooey perfection for the most incredible Three Cheese Macaroni and Cheese.
Three Cheese Perfection: Cheddar Cheese adds a tangy, nutty flavor. Mozzarella cheese adds a smooth texture with a great cheese pull. Colby Jack adds creaminess to the sauce for the ultimate trio of cheese for a great sauce.
Rich and Creamy: The cheese makes the ultimate sauce. The heavy cream, milk, and cheese combination makes a rich, hearty, and smooth sauce.
Family Friendly: Our Homemade Macaroni and Cheese is simple to prepare, and the instructions are so easy to follow. Perfection every time.

Ingredients you Need for 3 Cheese Mac and Cheese

Ingredients with text overlay for macaroni and cheese with three cheese choices.

An overview of the main ingredients. Full ingredient list and specifics in the recipe card below.

Small pasta shells - I always use small tube pasta that will hold the sauce, elbow, cavatappi, or medium shells called conchiglie all work well.
Sharp cheddar cheese - Through much recipe testing, sharp cheddar cheese adds a perfect flavor to the cheese sauce.
Mozzarella cheese - Mozzarella is a great melting cheese and adds a smoothness to the sauce. Not to mention, a great cheese pull for the sauce.
Colby Jack cheese - A great cheese to balance the sharpness of cheddar and the smoothness of mozzarella.
Unsalted butter - Use unsalted butter to control sodium.
Spices: smoked paprika - adds a nice color and smokiness to the cheese sauce. Garlic powder - adds a subtle flavoring to the cheese sauce.
Whole milk/ heavy cream warmed - After extensive recipe testing, this combination of milk and heavy cream yields the perfect sauce.
Dijon mustard - The mustard adds a nice kick with the spices and the variety of cheese.

Equipment needed for Homemade Macaroni and Cheese

9x13 inch casserole dish
Measuring Spoons and Cups
Stainless Steel Mixing Bowls
Whisk
8 Quart Pasta Pot
Cheese Grater

How to make Three Cheese Macaroni and Cheese

This is an overview of the recipe. The full instructions are below in the recipe card.

A large cast iron pan with all-purpose flour and butter to make a roux.

Make a roux with all-purpose flour and unsalted butter.

A cast iron Dutch oven with spices added to make a roux for Macaroni and Cheese.

Add the spices and whisk for 3 to 4 minutes to eliminate any flour flavor.

A creamy cheese sauce for macaroni and cheese with a spoon showing how the sauce coats the spoon for the perfect sauce.

Stir in the liquids and whisk until the mixture is thick, for at least 5 to 8 minutes. The sauce will coat a spoon.

A cast iron white Dutch oven with the a Bechamel sauce with shredded cheese to make a macaroni and cheese sauce.

Whisk in the cheese for the sauce.

A pasta pot with cooked macaroni topped with a cheese sauce.

Blend the pasta with the cheese sauce.

A white casserole dish with macaroni in a cheese sauce to make a creamy macaroni and cheese.

Layer the pasta and cheese sauce in the prepared casserole dish.

A white casserole dish with a baked homemade macaroni cheese.

Bake until bubbly, about 30 minutes.

Make-ahead, storage, and freezer tips

Make Ahead: The mac and cheese can be prepared up to 24 hours ahead and stored in the refrigerator- covered with aluminum foil or plastic wrap until ready to bake.

Storage - Leftover Homemade macaroni and cheese can be kept in an airtight covered container in the refrigerator for up to 3 days.

Reheating: Leftover baked mac and cheese can be reheated in a microwave or in an oven-safe baking dish at 325°F until warmed through.

Freezer-Friendly: Cool the mac and cheese. Place in a freezer-safe container or storage bag. It can be kept in the freezer for up to 3 months. Defrost in the refrigerator overnight before reheating.

Cooking the casserole from a frozen state: If the casserole is frozen, preheat the oven to 350°F/180°C. Cover the casserole with aluminum foil and bake for 45 minutes. Remove the aluminum foil, and continue baking until the mixture is bubbly and cooked through. This will be about 15 to 20 more minutes.

Creaminess: When reheating, if the sauce is dry, add a little milk or cream

A scoop of macaroni and cheese being picked up by a wooden spoon.

Eileen's Tips for the Best Macaroni and Cheese

Shred the cheese - Please buy a block of cheese and shred it yourself. Preshredded cheese has a coating on it, which prevents it from being a smooth sauce.
Use warm dairy. Use warm dairy for a smooth sauce.
Cheese Sauce: To ensure a smooth sauce, when the bechamel sauce is thick enough to add cheese, shut off the heat and add the shredded cheese in batches.
Undercook the pasta - I always boil the pasta for 3 minutes less than suggested on the box. The pasta will finish cooking when baked.
Taste testing - Always taste the cheese sauce for seasoning before adding it to the pasta. If needed, adjust any seasoning.
Toppings: If you prefer the cheese topping a bit crispy, place the baked macaroni casserole under the broiler for a few seconds. Be sure to watch it so you do not burn the top.
Don't overbake - Overbaking can dry out the sauce.

Homemade Mac and Cheese Recipe - Tips and Variations

Want to change up this recipe?

Pasta: I have used Gluten-free pasta from both Barilla and Ronzoni with success. Brown Rice Pasta or high-fiber pasta can also work via my recipe testing.
Milk: Low-fat milk worked for me with recipe testing. I tested with skim milk, and I do not love the flavor it adds to the sauce.
Inclusions: Any of these are great choices to add
- 1 cup steamed chopped broccoli
- 1 cup chopped cooked bacon
- 1 cup diced leftover ham
- 1 cup cooked peas
- 1 cup chopped cooked spinach
- 1 cup browned seasoned ground beef ( use salt and pepper)
Spices: Add a dash of nutmeg, onion powder, or chili powder.
Heat: Add a dash or two of hot sauce to the bechamel.

Toppings for Creamy Mac and Cheese

Melt 1 Tablespoon of unsalted butter and brown 1 cup of panko bread crumbs to add to the top of the macaroni and cheese for a crispy topping. These will also work:

plain bread crumbs
crumbled saltine crackers
crumbled butter crackers like Ritz crackers
crumbled cheddar Cheez-its

Best Cheese Combos for the Cheesiest Macaroni and Cheese

A cutting board with shredded cheese to make homemade three cheese macaroni and cheese.

The number one tip for making the best macaroni and cheese is to grate your cheese, as pre-shredded cheese has an anti-caking agent, making it difficult to melt.
Never use pre-shredded cheese as it contains a film which inhibits a smooth cheese sauce.
Cheese: Great choices of cheese are any combination of the following: Sharp Cheddar, Gruyère Cheese, Fontina, Gouda cheese, Monterey Jack, or any smoked cheese... so many options
Aged Cheese: If using Aged Parmesan, be sure to add it with another cheese, such as mozzarella or fontina, for better melting.
Cheese Combinations I have tried:
- Sharp Cheddar, Gruyere, Parmesan
- Fontina, Mozzarella, Gruyere
- Pepper Jack, Colby, Sharp Cheddar
- Gruyere, Fontina, Colby Jack

A four cheese combination:

Gruyère, Fontina, Gouda, Parmesan
Fontina, Gruyère, Colby Jack, and Cheddar
Smoked Gouda, Cheddar Cheese, Mozzarella, Parmesan Reggiano
Fontina, Smoked Gouda, Cheddar Cheese, Mozzarella

FAQs for the Best Three Cheese Macaroni and Cheese

Why is my cheese sauce grainy?

The cheese sauce can get grainy if you overheat the milk and cheese. Once the bechamel sauce is thick, remove the pot from the heat and gradually add the shredded cheese, stirring between each batch of additional cheese.

Can I use pre-shredded cheese?

Please grate your own cheese for the best cheese sauce. Preshredded cheese has a film on it, which makes it harder to melt.

Can I make the cheese sauce ahead of time?

Yes. Prepare the cheddar cheese sauce up to 24 hours ahead. Store the sauce in an airtight container in the refrigerator.
I prefer to reheat it for a few minutes on the stove before pouring it over the cooked pasta.

What to serve with Three Cheese Macaroni and Cheese

More Easy Pasta Recipes

Creamy Ham and Peas Pasta

Baked Spaghetti Casserole

Chicken Alfredo Linguine

More Macaroni and Cheese Recipes:

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Eileen xo

If you click on the number of servings in the recipe card, you can adjust the measurements up or down for the exact number of servings you need.

This recipe was originally published January 26, 2019. For user experience, we have updated the recipe and photos.

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Homemade macaroni and cheese being picked up out of a casserole dish.

Three Cheese Macaroni and Cheese

Our creamy Homemade Macaroni and Cheese is pure comfort food. It is easy to assemble with a luscious, silky, and smooth cheese sauce blended with tender, perfectly cooked pasta. We combine a perfect mix of sharp cheddar, mozzarella cheese, and Colby Jack cheese, that is a scrumptious sauce for macaroni and cheese.

5 from 1 vote

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Course: Main Dish

Cuisine: American

Keyword: macaroni and cheese recipe

Prep Time: 25

Cook Time: 30

Total Time: 55

Servings: servings

Calories: 366kcal

Author: Eileen Murphy Kelly

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Equipment Needed:

Ingredients

1 pound small pasta shells Note 1
2 cups sharp cheddar cheese
2 cups mozzarella cheese
2 cups Colby jack cheese
4 Tablespoons unsalted butter note 2
4 Tablespoon all-purpose flour Note 3
1 teaspoon salt
½ teaspoon black pepper
½ teaspoon smoked paprika
½ teaspoon garlic powder
2 cups whole milk, warmed Note 4
2 cups heavy cream, warmed Note 4
½ teaspoon Dijon mustard
non-stick cooking spray

US Customary - Metric

Instructions

Pre-heat oven to 375°F. Spray a 9 x 13-inch baking dish with non-stick cooking spray, set aside.
Cook 1 pound small pasta shells pasta in a large pot of salted boiling water, according to package, reduce cooking time by 3 minutes.
While the pasta is cooking, grate and mix together 2 cups sharp cheddar cheese, 2 cups mozzarella cheese, and 2 cups Colby jack cheese into a large bowl. Separate into 4 cup of cheese for the cheese sauce, 1 cup of cheese for the middle of the casserole, and 1 cup of cheese for topping the casserole.
In a medium-sized sauce pot, over medium heat, melt 4 Tablespoons unsalted butter. Whisk in 4 Tablespoon all-purpose flour, 1 teaspoon salt, ½ teaspoon black pepper, ½ teaspoon smoked paprika, and ½ teaspoon garlic powder, whisk for 1-2 minutes to blend the ingredients and cook out the flavor of the flour.
Make a bechamel sauce; increase heat to medium-high, add 2 cups whole milk, warmed 2 cups heavy cream, warmed, and ½ teaspoon Dijon mustard, continue to whisk until mixture becomes thick and bubbly. When thick enough, the mixture should be able to coat the back of a spoon. Remove the pot from the heat. Taste the sauce for seasoning, if needed, adjust any seasonings.
To make the cheese sauce, add 4 cups of the cheese mixture to the bechamel sauce. Whisk to combine ingredients until smooth.
In a pan used to make the pasta, add back in the cooked pasta and cheese sauce. Mix until well combined.
To the prepared baking dish, add ½ of the pasta/cheese mixture. Sprinkle the top with 1 cup of the cheese mixture.
Add the remaining pasta/cheese mixture and sprinkle with the remaining 1 cup of cheese.
Cover with aluminum foil and bake in the preheated oven for 20 minutes. Remove aluminum foil and continue to bake about 5-10 minutes to melt remaining cheese. The mixture will be bubbly.
Optional: If you love a crispy topping; turn the broiler to high and return the casserole to the oven under the broiler setting for about 1 minute, the topping will brown slightly.
Ready to serve with optional garnishes; crumbled bacon, panko bread crumbs, or fresh herbs.

NOTES

Be sure to check the Expert Tips and FAQs above for important tips and questions that can help make a delicious recipe.

Note 1: Small pasta shells will work.

Note 2: If only salted butter is available, reduce the salt to ¼ teaspoon.

Note 2: Gluten free flour can be used. I find Bob's Red Mill One to One Flour works well.

Note 4: Warming the milk before adding to the butter/flour mixture ensures a creamy sauce. The flour mixture won't clump.

I'm not a registered dietitian, but I strive to provide the most accurate nutritional values. Any nutritional data I provide is an approximation. Actual dietary information can vary based on ingredients and portion sizes.

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Nutrition

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