Butternut Squash Healthy Mac And Cheese | Make It Healthy

This healthy mac and cheese recipe uses butternut squash, unrefined flour, greek yogurt, and all clean eating ingredients to make the best healthy mac and cheese ever!  This is the NUMBER ONE recipe I get asked to #makeithealthy!

Healthy Mac And Cheese | This healthy mac and cheese recipe uses butternut squash, unrefined flour, greek yogurt, and all clean eating ingredients to make the best healthy mac and cheese ever!  This is the NUMBER ONE recipe I get asked to #makeithealthy! | A Sweet Pea Chef

First and foremost, I’d like to just say how incredibly awesome I think you are.

Over the years of running this blog, Dustin and I have experienced several highs and lows.  To be honest, at certain times in the past, it was a struggle to keep it going. And, at other times, it’s been such an amazing experience – one I couldn’t imagine not having in my life.

But, I’ve gotta say, when I asked the question on Instagram and Facebook of what you would like me to “make healthy,” that was definitely one of the coolest moments we’ve ever experienced. Literally, within less than 30 minutes, we had like, 100 requests for favorite recipes that you wanted me to make into a healthier version.

I was floored.  How cool!

Casserole dish with healthy mac and cheese which has been spooned out with a wooden spoon.

How To Make Mac And Cheese Healthy

One of the most common requests we have received has been for a healthy mac and cheese recipe.  So, how do you make a healthy mac and cheese?  Here’s how we did it:

  • Use butternut squash, greek yogurt, parmesan cheese, and chickpea flour to make a creamy “cheese sauce”
  • Use gluten-free, refined flour free, high-fiber, high-protein noodles instead of regular macaroni noodles
  • Replace refined all purpose flour with chickpea flour to thicken the sauce
  • Use plain greek yogurt to add tartness, creaminess, and thickness to replace a lot of the cheese
  • Remove all the butter
  • Replace whole milk and/or heavy cream with a combination of unsweetened almond milk and low sodium chicken broth
  • Replace breadcrumbs with almond meal

Not only is this healthy mac and cheese recipe clean-eating, it’s also delicious, easy, and a great new way to enjoy an old favorite.

I hope you enjoy it as much as we did and, again, THANK YOU so much for your support and your awesomeness!

Close up shot of a fork taking a big bite of the healthy mac and cheese, which shows the golden edges of the noodles.

Can This Healthy Mac And Cheese Recipe Be Made Ahead?

This clean eating mac and cheese recipe can be made ahead, but I recommend that it not be baked until you’re ready to eat it.  The noodles may break down some, as they are unrefined quinoa noodles, but they will still taste great.

Just prep everything ahead of time, then either store in the refrigerator or freeze until ready to bake. When it’s time to bake, follow the directions below.  It can be thawed in the refrigerator overnight if frozen.

Healthy mac and cheese that has been baked and contains quinoa noodles covered in a butternut squash cheese sauce to make it a clean eating mac and cheese.

How To Make Healthy Butternut Squash Sauce For Mac and Cheese

I mentioned earlier I replaced your regular cheese and flour mac and cheese sauce with butternut squash.  A lot of people ask me how to do this and does it really compare to the real mac and cheese.  So, I figured I’d talk a little more about how to make butternut squash sauce for mac and cheese.  For starters, here are the ingredients you’ll need:

  • butternut squash

  • yellow onion

  • garlic

  • almond milk

  • low-sodium chicken broth

  • plain greek yogurt

  • sea salt

  • black pepper

  • chickpea flour

See?  Super simple ingredient list for the butternut squash sauce.  Then, to make it, just follow these easy steps:

  1. Add the cubed butternut squash, onion, garlic, almond milk, and chicken broth to a deep pot and cook over medium-high heat. Allow to simmer until the butternut squash is tender.
  2. Once tender, carefully transfer the butternut squash contents to a blender and purée until very smooth. This process may require you to blend in batches.
  3. Add 1/2 tsp. sea salt, 1/2 tsp. ground black pepper, the greek yogurt, and the chickpea flour and blend again. Taste for seasoning and add any additional salt or pepper as needed.
  4. Pour the butternut squash mixture over the noodles and stir to incorporate.

So easy and simple!

CAN I MAKE HEALTHY MAC AND CHEESE ON STOVE TOP?

Yes, this healthy mac and cheese recipe works as a stove top creation, too. You’ll miss the savory and crumbly topping but the creaminess of this scrumptious dish makes up for it.

HOW CAN I MAKE HEALTHY MAC AND CHEESE NON-DAIRY OR VEGAN?

Healthy Mac and Cheese can easily be converted to a vegan or non-dairy dish. 

  • As a replacement for the Greek yogurt, try a plant-based yogurt. Flavorful and easy to work with, plant-based yogurts are healthy for the digestive system and contain antioxidants, protein, vitamins, minerals, and lots more good-for-you ingredients!
  • Use vegan parmesan in place of the regular parmesan; you won’t miss a thing.
  • Instead of using chicken broth in the sauce, incorporate a low-sodium vegetable broth.

HOW CAN I MAKE HEALTHY MAC AND CHEESE NUT-FREE?

To make this yummy Mac and Cheese dish in a nut-free format, do the following:

  • Replace the almond milk for rice milk – it’s neutral in flavor like the almond milk so works well
  • Switch the almond meal for sunflower seed meal for a great substitute

WHAT CAN I USE INSTEAD OF BUTTERNUT SQUASH IN HEALTHY MAC AND CHEESE?

Instead of using squash in this healthy Mac and Cheese dish, you can use acorn squash or sweet potatoes and still end up with a tasty dish! Really, any winter squash works well as long as you purée it to a smooth consistency. This will ensure you end up with a creamy-textured sauce.

I can’t tell you how much I appreciated all the excitement and encouragement you shared with me then and continue to share with me now.  It is just so awesome to be part of this community and to be here to help make these recipes we all know and love be super tasty and GOOD for us.

Because why the heck not, right? Why NOT make our favorite foods healthy? Why NOT take back our health?

What recipe would YOU like me to #makeithealthy next?  Share in the comments below!  If we pick your idea, we’ll send you a free A Sweet Pea Chef t-shirt and make your recipe!    Plus: all the cool kids are doing it.

LOOKING FOR MORE HEALTHY PASTA RECIPES?

If pasta is your passion and you want to keep it healthy, try some of my favorite go-to dishes:

Healthy Mac and Cheese

5 from 3 votes
Healthy Mac And Cheese Square Recipe Preview Image
Healthy Mac And Cheese | Make It Healthy
Prep Time
25 mins
Cook Time
25 mins
Total Time
50 mins
 

This healthy mac and cheese recipe uses butternut squash, unrefined flour, greek yogurt, and all clean eating ingredients to make the best healthy mac and cheese ever!

Categories: Clean, gluten free, Healthy, Kid-Friendly, Vegetarian
Difficulty: Easy
Keyword: healthy mac and cheese, healthy mac and cheese recipe, low calorie mac and cheese
Servings: 8
Calories: 287 kcal
Author: Lacey Baier of A Sweet Pea Chef
Ingredients
  • 16 oz quinoa noodles (2 boxes)
  • 3 cups butternut squash (approx. 1/2 squash), cubed
  • 1/2 yellow onion, diced
  • 2 cloves garlic, minced
  • 1 1/2 cups plain almond milk
  • 1 1/2 cups low sodium chicken broth
  • 1/2 cup plain greek yogurt
  • 1 1/2 tsp sea salt, divided
  • 3/4 tsp black pepper, divided
  • 1 tbsp chickpea flour
  • 1/4 cup parmesan, grated
  • 1/4 cup almond meal
  • 1/4 tsp garlic powder
Instructions
  1. Preheat oven to 350 degrees.
  2. Fill a deep pot with water and bring to a boil. Once boiling, add the quinoa noodles and cook until almost tender, about 6-7 minutes.

  3. While the noodles are cooking, add the cubed butternut squash, onion, garlic, almond milk, and chicken stock to another pot and cook over medium-high heat. Allow to simmer until the butternut squash is tender.

  4. In a small bowl, combine the parmesan cheese, almond meal, remaining 1/2 tsp. sea salt, remaining 1/4 tsp. pepper, and garlic powder and mix well. Set aside.

  5. Once tender, carefully transfer the butternut squash contents to a blender and puree until very smooth. This process may require you to blend in batches.

  6. Add 1/2 tsp. sea salt, 1/2 tsp. ground black pepper, the greek yogurt, and the chickpea flour and blend again. Taste for seasoning and add any additional salt or pepper as needed.
  7. Drain the cooked noodles and return to the pot.
  8. Pour the butternut squash mixture over the noodles and stir to incorporate.
  9. Pour the macaroni and cheese mixture into a casserole dish.

  10. Sprinkle the parmesan mixture evenly over the top of the mac and cheese.
  11. Place into the oven and bake for 20-25 minutes, or until the top is golden brown.

Recipe Video

Nutrition Facts
Healthy Mac And Cheese | Make It Healthy
Amount Per Serving (1 cup)
Calories 287 Calories from Fat 36
% Daily Value*
Fat 4g6%
Saturated Fat 1g5%
Cholesterol 3mg1%
Sodium 568mg24%
Potassium 258mg7%
Carbohydrates 55g18%
Fiber 2g8%
Sugar 2g2%
Protein 9g18%
Vitamin A 5605IU112%
Vitamin C 12mg15%
Calcium 144mg14%
Iron 1mg6%
* Percent Daily Values are based on a 2000 calorie diet.

This post contains affiliate links for products I use regularly and highly recommend.

Lacey Baier

Hey y’all, I’m Lacey Baier and I’m so glad you’re here! I’m a healthy lifestyle influencer and the creator of this clean-eating blog and YouTube channel, A Sweet Pea Chef. My recipes have been published on Food Network, Good Morning America, FoxNews, Tastemade, Fitness Magazine, and much more. I live in Dallas, Texas with my husband and four kiddos. Let’s get started!

18 thoughts on “Butternut Squash Healthy Mac And Cheese | Make It Healthy

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  2. Wow! I really liked it! Thank you for this infomation, now i would like to read about it in details! And also i invite you here above.

  3. 5 stars
    Delicious!!! Had to use chick pea pasta for quinoa pasta, and had to substitute almond flour for chick pea flour. The butternut sauce looked like cheese sauce, yogurt tones down the orange color. I love Mac and cheese but have avoided it- love this recipe!! Looking forward to trying healthy green bean casserole!!!

  4. This might be a stupid question, but does the sauce taste like butternut squash at all? For some reason, butternut squash is the one veggie I just can’t stand ha.

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