Healthy Mac and Cheese Recipe

Published by:
Liz Marino
| 10/04/2022 | Last Updated: 04/24/2025

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This Healthy Mac and Cheese Recipe is easy to make and delicious! A low calorie mac and cheese that is creamy, baked and yummy!

An overhead shot of a blue bowl of healthy mac and cheese on a grey background


 

Doesn’t everyone love a helping of mac and cheese with delicious creamy sauce? It’s such an ultimate comfort food, but let’s be honest – most mac and cheese recipes are not exactly healthy.

That’s why we’re so excited about this healthy mac and cheese recipe. Just like our Healthier Alfredo Sauce and Lighter Chicken Pot Pie, we’ve taken a classic comfort dish and made it better for you with real, simple ingredients—without sacrificing the flavors we all love.

We mix cheddar cheese and parmesan cheese for a rich, creamy sauce lightened up with skim milk instead of heavy cream, which results in a creamy, satisfying sauce that feels indulgent but is so much lighter than your traditional mac and cheese.

In only 30 minutes, you can have a high protein side (19g per serving) that’s perfect for a weeknight dinner or a holiday table. Plus, it’s a major upgrade from the boxed stuff, which is often packed with preservatives and artificial ingredients.

Liz’s secret for the best healthy mac and cheese

  • Grate your own cheese! I know it’s tempting to grab a bag of pre-shredded cheese, but freshly grated cheese melts so much better—and gives you the cheesiest, creamiest mac and cheese. Pre-shredded cheese is coated with preservatives and anti-caking agents to make it last longer and prevent it from melting as smoothly. Taking a few extra minutes to grate your own is totally worth it!

Ingredients

Ingredients for healthy mac and cheese in white bowls: elbow macaroni pasta, olive oil, onion, all purpose flour or gluten free, skim milk, garlic, shredded cheddar cheese, parmesan cheese, salt & pepper, breadcrumbs, dried basil, dried parsley, dried oregano, melted butter

Substitutions

Pasta: Any short grain pasta will work in this recipe. Rotini, elbow noodles, or orecchiette work great! Chickpea pasta or whole wheat pasta may work, but I haven’t tried them so I can’t be sure.

Olive Oil: You can substitute olive oil with avocado oil, melted butter, or ghee.

Onion/Garlic: These are essential for flavor! If you don’t have fresh onion or garlic, used 1/2 teaspoon of garlic powder and onion powder.

Flour: Gluten Free flour may be used in place of all purpose flour to make this cheese sauce gluten free. You could also try this Gluten-free Mac and Cheese.

Cheddar Cheese: Feel free to use sharp cheddar cheese. You can substitute additional parmesan cheese instead of cheddar cheese for the cheese sauce but it will not be as creamy. This will lower the lactose levels, possibly making it easier on your stomach! We don’t recommend making this with dairy free cheese. It doesn’t melt as well. We also don’t recommend doing this with low fat cheese.

Milk: To make this healthier mac and cheese recipe with less lactose and dairy, you can use unsweetened almond milk or oat milk. Skim milk, whole milk, or half and half will work.

Lower Salt: Cheese is inherently salty. Unfortunately, this is a higher salt recipe but we believe everything is ok in moderation. This is still lower in salt than most mac and cheese recipes.

What can I add to my mac and cheese? You can add buffalo sauce, chiles, peppers or chopped spinach to your mac and cheese if you’d like!

How to Make Healthy Mac and Cheese

Pasta and cheese sauce tossed together in a black pot on a grey background for healthy mac n cheese
  1. In a sauté pan, add olive oil, onions, garlic, and pepper. Once cooked, add in flour until a thick paste starts to form. Add milk, constantly stirring until the cheese sauce mixture is thick and creamy. Add both kinds of cheese, stir, then mix in pasta.
A white bowl of the breading topping for healthy mac and cheese
  1. In a separate bowl, mix breadcrumbs, butter, cheese and spices.
A blue casserole dish with healthy mac and cheese before being baked
  1. Pour into a greased baking dish. Top the pasta with the breadcrumb mixture.
A blue casserole dish with healthy mac and cheese after being baked
  1. Bake at 400° uncovered for 15-20 minutes until bread crumbs are golden brown.
A scoop of healthy mac and cheese being taken out of a blue casserole dish

Serving Suggestions

You can eat this mac and cheese by itself or it is a delicious side to so many dinners! Here are some of our favorite dinners to pair it with:

A close shot of a blue bowl of healthy mac and cheese on a grey background

Baked Mac and Cheese FAQ

Is Mac and Cheese Healthy?

We believe everything is ok in moderation. This healthy mac and cheese recipe is higher in calories, carbs, and salt than most of our healthy sides; however, if you are craving mac and cheese, this is a better option for you than a traditional recipe!

What cheese is best in mac and cheese?

We like cheddar cheese and parmesan cheese for the most delicious creamy sauce!

How to Store

Storing: This mac and cheese will last in the refrigerator for up to 4 days in an airtight container

Freezing: We don’t recommend freezing healthy mac and cheese. Pasta can get really mushy in the freezer.

Reheating: You can reheat this healthy macaroni and cheese recipe in the microwave, toaster oven, oven, or on the stove.

A fork taking a bite of healthy mac and cheese out of a blue bowl on a grey background
An overhead shot of a blue bowl of healthy mac and cheese on a grey background

Healthy Homemade Mac and Cheese

Recipe by: Liz Marino
4.10 from 21 votes
This Healthy Mac and Cheese Recipe is easy to make and delicious! A low calorie mac and cheese that is creamy, baked and yummy!
Prep Time : 5 minutes
Cook Time : 30 minutes
Serves : 8 1 cup servings
(hover over # to adjust)

Ingredients

Pasta

  • 1 lb elbow macaroni pasta
  • 1 tablespoon olive oil
  • 3/4 cup onion diced
  • 2 tablespoons all purpose flour or gluten free
  • 1 – 1½ cup skim milk
  • 1/2 tablespoon minced garlic
  • 1 cup shredded cheddar cheese
  • 1 cup grated parmesan cheese
  • 1/4 teaspoon black pepper

Breadcrumb topping

  • 1/2 cup breadcrumbs
  • 1/4 cup grated Parmesan cheese
  • 1/4 teaspoon dried basil
  • 1/4 teaspoon dried parsley
  • 1/4 teaspoon dried oregano
  • 2 tablespoons melted butter

Instructions

  1. Preheat oven to 400 degrees.
  2. In a pot, start to boil water for pasta. Once boiling, add pasta and cook the past to al dente – about 1-2 minutes less than according to the package.
  3. In a sauté pan, add extra virgin olive oil, onions, garlic and pepper. Cook until soft and golden brown – about 5 minutes.
  4. Once cooked, gradually add in flour until thick paste starts to form. Gradually add milk, stirring constantly until the cheese mixture is thick and creamy.
  5. Add both cheeses and stir.
  6. Toss the cooked pasta with the cheese sauce. Pour into a greased 8×8 baking dish.
  7. In a separate bowl, mix breadcrumbs, butter, cheese and spices. Top the pasta with the breadcrumb mixture.
  8. Bake in the oven uncovered for 15-20 minutes until bread crumbs are golden brown.

Video

Youtube video

Nutrition Facts

Serving: 1cup | Calories: 439kcal | Carbohydrates: 56g | Protein: 19g | Fat: 15g | Saturated Fat: 7g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 4g | Trans Fat: 0.1g | Cholesterol: 37mg | Sodium: 469mg | Potassium: 329mg | Fiber: 2g | Sugar: 7g | Vitamin A: 518IU | Vitamin C: 1mg | Calcium: 377mg | Iron: 1mg
Course: Main Course
Cuisine: American
Tried this recipe?Share it! Make sure to tag @thecleaneatingcouple or use #thecleaneatingcouple!
4.10 from 21 votes (15 ratings without comment)

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Recipe Rating




6 Comments

  1. 4 stars
    Not too bad, just a little dry and I even used a little less pasta too. I liked the topping a lot. Will just add more milk next time and for leftovers.

  2. Charlotte Dawson says:

    3 stars
    It has potential, the topping is lovely but it came out SO dry sorry and I followed the recipe to a t! Perhaps less pasta and it would have been okay….

  3. 5 stars
    Great recipe, easy to prepare, delicious! Enough for two meals.

  4. 5 stars
    Added diced jalapeños. Delicious!

  5. 5 stars
    So I made the roux wrong and it was really soupy but I’m not a chef and I didn’t want to add flour and think it would fix it so I just kept moving forward…so with that information, all the cheese flavoring was at the bottom and left the top really dry. BUT, I mixed it all up after the first bowl and it was really good. The flavoring was there, I just needed to mix it half way through baking but with the topping I couldn’t. I will be attempting this again…the roux – you have not defeated me!!

  6. Lynne Falcigno says:

    5 stars
    So good! Comfort food at its best!