• Skip to primary navigation
  • Skip to main content
  • Skip to primary sidebar
A Sweet Pea Chef
  • Recipes
  • Meal Prep
  • My Story
  • Coaching
  • Cookbook
menu icon
go to homepage
  • Recipes
  • Meal Prep
  • My Story
  • Coaching
  • Cookbook
subscribe
search icon
Homepage link
  • Recipes
  • Meal Prep
  • My Story
  • Coaching
  • Cookbook
×
You are here: Home » Recipes » Healthy Casseroles

Butternut Squash Healthy Mac And Cheese | Make It Healthy

Updated: Dec 13, 2024 · Published: Apr 28, 2017 by Lacey Baier · This post may contain affiliate links which won’t change your price but will share some commission. · 19 Comments

Jump To Recipe!

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!

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! this RECIPE

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!

Overhead view of a 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
  • 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 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 ½ tsp. sea salt, ½ 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!

HOW TO MAKE IT ON THE STOVETOP

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

HOW TO MAKE 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.
  • 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 TO MAKE 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

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 Quinoa Make Ahead Casserole
  • Sweet Potato Lasagna
  • Turkey Meatballs With Spaghetti Squash Noodles

Healthy Mac and Cheese

Healthy Mac and Cheese

Healthy Mac And Cheese | Make It Healthy

Lacey Baier
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!
4.75 from 4 votes
Print Recipe Pin Recipe
Prep Time 25 minutes mins
Cook Time 25 minutes mins
Total Time 50 minutes mins
Course Side
Cuisine American
Servings 8
Calories 287 kcal

Equipment

  • Stock Pot or Large Deep Skillet
  • mixing bowl
  • casserole dish

*This post may contain affiliate links for products I use often and highly recommend.

Ingredients
  

  • 16 oz quinoa noodles (2 boxes)
  • 3 cups butternut squash (approx. ½ squash), cubed
  • ½ yellow onion, diced
  • 2 cloves garlic, minced
  • 1 ½ cups plain almond milk
  • 1 ½ cups low sodium chicken broth
  • ½ cup plain greek yogurt
  • 1 ½ teaspoon sea salt, divided
  • ¾ teaspoon black pepper, divided
  • 1 tablespoon chickpea flour
  • ¼ cup parmesan, grated
  • ¼ cup almond meal
  • ¼ teaspoon garlic powder

Instructions
 

  • Preheat oven to 350 degrees.
  • 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.
  • 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.
  • In a small bowl, combine the parmesan cheese, almond meal, remaining ½ tsp. sea salt, remaining ¼ tsp. pepper, and garlic powder and mix well. Set aside.
  • 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.
  • Add ½ tsp. sea salt, ½ 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.
  • Drain the cooked noodles and return to the pot.
  • Pour the butternut squash mixture over the noodles and stir to incorporate.
  • Pour the macaroni and cheese mixture into a casserole dish.
  • Sprinkle the parmesan mixture evenly over the top of the mac and cheese.
  • Place into the oven and bake for 20-25 minutes, or until the top is golden brown.

Video

Nutrition

Serving: 1 cupCalories: 287 kcalCarbohydrates: 55 gProtein: 9 gFat: 4 gSaturated Fat: 1 gCholesterol: 3 mgSodium: 568 mgPotassium: 258 mgFiber: 2 gSugar: 2 gVitamin A: 5605 IUVitamin C: 12 mgCalcium: 144 mgIron: 1 mg
DID YOU MAKE THIS RECIPE?Tag @asweetpeachef on Instagram so we can check it out.

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

« Quinoa Lentil Salad with Lemon Vinaigrette
Stuffed Spaghetti Squash Bowls »

Reader Interactions

Comments

    4.75 from 4 votes (1 rating without comment)

    Leave a Comment Cancel reply

    Your email address will not be published. Required fields are marked *

    Recipe Rating




    This site uses Akismet to reduce spam. Learn how your comment data is processed.

  1. Allie

    August 14, 2020 at 4:04 pm

    This used to be a recipe for THE BEST Mac and cheese.. Full fat not healthy with butternut squash. The recipe was on my Pinterest for years, then one day it was replaced with this recipe. WHERE IS THE OTHER RECIPE??? I know this is the same link to the recipe because I sent it to tons of people who wanted it more than a year ago, and when I click it from their text message it brings me here.

    Reply
    • Michelle B

      November 26, 2020 at 12:00 am

      Yeah....I need the old recipe!! Where can we find that? I bring it to Thanksgiving and Christmas every year and now it’s just GONE!

      Reply
  2. Jann

    November 23, 2019 at 10:15 pm

    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!!!

    Reply
  3. Mary

    January 11, 2019 at 7:35 pm

    I am allergic to tree nuts. What is a good substitute or should I use panko or something?

    Reply
    • Lacey Baier

      November 12, 2019 at 6:50 pm

      You could use chickpea flour or Panko for sure. The Pablo isn’t clean eating but it’s def a better option for you than nuts.

      Reply
  4. Anna

    November 07, 2018 at 1:42 pm

    5 stars
    Where do you get inspiration for your recipes? Every dish looks delicious and I can not wait to taste it <3

    Reply
    • Lacey Baier

      November 12, 2019 at 6:51 pm

      I try to keep an open mind about ingredients and how they can be used in different ways. I’m so glad my recipes are impressive and inspiring to you. 🙂

      Reply
  5. Jo-Ann Grigor

    October 30, 2018 at 1:25 pm

    do you have a receipt for the almond meal ?

    Reply
    • Lacey Baier

      November 12, 2019 at 6:49 pm

      No, I don’t yet. So sorry!

      Reply
    • Heather Harper

      April 05, 2021 at 2:18 pm

      So I just took raw almonds amd put them in a food processor an grounded them up till real fine snd that was my almond meal.. saw online that you found easily do this so I gave it a go.. worked fine for me..

      Reply
  6. Anna Harrison

    January 04, 2018 at 10:18 am

    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.

    Reply
    • Lacey Baier

      January 04, 2018 at 8:04 pm

      It actually doesn't. My kids can't tell the difference 🙂

      Reply
  7. Dustin

    April 28, 2017 at 12:39 pm

    5 stars
    We should make this again. Everyone seemed to enjoy it 🙂

    Reply
    • Lacey Baier

      January 03, 2018 at 9:43 pm

      Yea, it's so sneaky and so good!

      Reply

Primary Sidebar

Lacey Baier Weight Loss Coach drinking a smoothie and smiling

HEY THERE!

I'm Lacey! Nice to meet you 🙂

I’m a Cleanish Lifestyle Coach, YouTuber, and Blogger. I live in Austin, TX with my husband, 4 kids, and 2 mini Aussies. I'm here to help you transform your life through delicious clean eating recipes and science-backed knowledge!

Learn more →

newsletter image that promotes the cleanish square a newsletter focused on eating healthy and making good choices

New Year, New You!

  • peaches in a bowl
    How to Freeze Peaches (For Smoothies!)
  • Top 14 Healthy Soda Swaps written in text with healthy homemade soda in the background of various colors.
    Top 14 Healthy Soda Alternatives
  • lacey holding up an iced caffe americano to demonstrate a healthy starbucks drink
    Top 10 Healthiest Starbucks Drinks (Hot and Cold) + How To Order Healthy At Starbucks!
  • Do Vitamins Break Your Fast? AVOID These 6 Supplements That Are Breaking Your Fast
  • Do ACV Gummies Work?
    Do ACV Gummies Work?
  • Lacey before and after thumbnail
    4 Tips From a Weight Loss Coach (Who's Actually Been There)

Popular Recipes

  • high protein fruit smoothies all lined up in a row
    5 High Protein Fruit Smoothie Recipes
  • Top down photo of 7 day meal prep
    7-Day Meal Prep For Weight Loss
  • meal prep for inflammation
    5-Day Anti-Inflammatory Diet Meal Plan
  • Banana Protein shake
    Banana Protein Shake
  • side view of healthy creamers in a row
    How to Make Coffee Creamer + 5 Easy Coffee Creamers
  • top down view of slow cooker chicken meal prep
    Slow Cooker Shredded Chicken

Most Popular

  • 130+ Meal Prep Ideas
  • 25+ Protein Smoothie Ideas
  • How To Meal Prep
  • Ultimate Guide to Meal Prep Containers
  • Benefits Apple Cider Vinegar
  • How To Quit Sugar
  • Ultimate Smoothie Guide
  • Meal Prep For Weight Loss
Cleanish Protein Ad
Lacey Baier Cook Book Waiting List

Footer

↑ back to top

Sweet Pea Chef

  • Subscribe
  • Recipes
  • About
  • Cookbook
  • Contact
  • FAQ
  • Shop

Recipes

  • Paleo Recipes
  • Gluten-Free Recipes
  • Keto Recipes
  • Vegan Recipes
  • Instant Pot Recipes
  • Slow Cooker Recipes
  • Soup Recipes
  • Videos

As an Amazon Associate, I earn from qualifying purchases.

Copyright © 2024 Cleanish LLC

Privacy Policy Terms Editorial Policy

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! | A Sweet Pea Chef
  • 87

Rate This Recipe

Your vote:




A rating is required
A name is required
An email is required

Recipe Ratings without Comment

Something went wrong. Please try again.