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Homemade Macaroni and Cheese

Homemade Macaroni and Cheese – My kids love eating homemade macaroni and cheese, especially when it’s creamy, “cheesy” and very satisfying. This comfort dish is the perfect recipe for dinner and next day leftovers.

homemade macaroni and cheese

A Healthier Version of Homemade Macaroni and Cheese

If you’re familiar with Clean Cuisine, then you know that we have some clean eating standards. We find every way possible to add extra vegetables and nutrients to our dishes whenever we can. While avoiding gluten, dairy and refined sugar.

Here are a 5 things that make this homemade Macaroni and Cheese super healthy!

#1: Use Gluten Free Pasta – Try Chickpea, Vegetable-based or Brown Rice Pasta

Our pantry is stuffed with pasta options because we are always trying new brands. We love the new Banza chickpea pasta that can be found at Target or Thrive Market. Also, started enjoying Jovial brand, also found at Thrive Market or your local Wegman’s.

For this recipe, I used Jovial brown rice shell pasta and it was perfectly delicious. I cooked it follow the instructions versus al dente. This homemade macaroni and cheese recipe does go in the oven for a few minutes. However, it’s not enough time to really cook the pasta much.

#2: Use Cashew Cream to Make it Dairy Free

Soak raw cashews in hot water for 1 hour, strain and add to a blender makes this sauce creamy. Creamy cashews easily replicate a cheesy sauce that is PERFECT for this recipe for homemade macaroni and cheese.

Go with raw cashews — and don’t forget to soak them. You can use hot, boiling water for 1 hour or feel free to soak overnight. The softer the cashews, the creamier the sauce.

homemade macaroni and cheese

#3: Butternut Squash for a Win!

To make the sauce creamy for this homemade macaroni and cheese recipe, I used 1 cup of roasted butternut squash. You can absolutely use frozen butternut squash, but we LOVE the texture, flavor and dark color of roasted butternut squash.

Plus, there’s an incredible amount of vitamins, minerals and disease-fighting antioxidants from eating butternut squash. Naturally, this squash is low in calories and rich in fiber. It can also protect against cancers, heart diseases and adds so much to this homemade macaroni and cheese.

Guess what? If you don’t have any cashews, toss in an extra cup of butternut squash. I’ve done this before and it was still so delicious. But, we do love the creaminess of the cashews!

#4: Truffle Oil Adds a Load of Flavor

Have you ever enjoyed truffle fries from a local restaurant. The flavor that just a little bit of truffle oil offers is amazing. In this recipe, we added just 1 tablespoon of truffle oil and that’s all you need. Yes, it can be a little pricey to pick up, but it’s the perfect umami-flavored addition to this recipe.

If you don’t have truffle oil – or don’t care for the taste, you can always use cold pressed extra virgin olive oil.

#5: Nutritional Yeast is Packed with Nutrients

Nutritional yeast is used in this homemade macaroni and cheese recipe and is nutrient-packed. You can pick up a bag or jar at most healthy food stores or Amazon, of course. We love Bragg’s or Bob’s Red Mill — you can’t go wrong with either one.

Nutritional yeast is different than baking yeast. Nutritional yeast is is inactive which means that it does not feed on sugars or promote candida. For this reason, those who are advised to avoid yeast, can almost always tolerate nutritional yeast.

Not only is nutritional yeast a complete protein source for vegans, but it’s also a rich source of b12. Plus it tastes delicious! Using nutritional yeast in this recipe for homemade macaroni and cheese provides a mild cheddar cheese flavor. It allows this recipe to use much less cheese while still being full of flavor.

homemade macaroni and cheese

Dairy Free Homemade Macaroni and Cheese

Yes, creating a healthy homemade macaroni and cheese recipe that actually tastes good is easier said than done. But now we know, it can be done!

For the past year, I’ve made numerous changes this to this recipe to make it as tasty as it is. Not only is this homemade macaroni and cheese taste delicious, but it’s loaded with nutrients.

If you want to use cheese, we suggest just a little bit! 1 cup of organic grass-fed extra sharp cheese is all that is needed. This is equivalent to about 2 tablespoons per serving. Of course, if you are wanting to make this completely dairy free, use a dairy free cheese!

Make a Big Batch of Homemade Macaroni and Cheese

This recipe easily makes a jumbo serving of homemade macaroni and cheese. For a family of 4, you can expect to get at least 2 meals out of it. We typically eat it for dinner the first night and then lunch the second day.

Leftovers can be stored in a covered container in the fridge for up to 3 days.

homemade macaroni and cheese

Love Spicy Food? Try this on your Macaroni and Cheese!

Being a native western New York girl, I was raised with buffalo wings and hot sauce. So, when Nana Cathy insisted we add a little hot sauce and rotisserie chicken to our macaroni and cheese, I knew I had to try it.

Sure enough, she was onto something here.

So, if you love a little spicy kick to your homemade macaroni and cheese, be sure to add a little Texas Pete® Hot Sauce. You can easily use rotisserie chicken or grilled pastured boneless, skinless chicken thighs. We stack it all together and put our chicken and hot sauce right on top of our homemade macaroni and cheese.

A genuine bowl of comfort food.

Now, for that delicious, healthy homemade macaroni and cheese recipe using butternut squash, cashews and nutritional yeast!

Bon appetit!


Homemade Macaroni and Cheese

Homemade Macaroni and Cheese is a perfect comfort food. Our recipe uses gluten free pasta and a dairy free creamy sauce.

homemade macaroni and cheese
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  • Prep Time: 30 minutes
  • Cook Time: 15 minutes
  • Total Time: 45 minutes
  • Yield: 12 1x


  • 1 cup roasted butternut squash, see notes below
  • 1 cup raw cashews, soaked in hot water for 1 hour
  • 2 tablespoons fresh lemon juice
  • ½ cup water
  • 1 tablespoon truffle oil, or use extra virgin olive oil
  • ½ teaspoon unrefined sea salt
  • ¼ cup nutritional yeast, such as this one from Bragg’s
  • ¼ teaspoon cayenne pepper
  • 1 teaspoon smoked paprika
  • 6 cups cooked chickpea pasta or gluten free pasta

OPTIONAL: 1 cup organic sharp cheddar, to make this dairy free, use dairy free organic cheese


  1. Preheat the oven to 350 degrees.
  2. Prepare pasta according to instructions. Strain the pasta and add to a large pot, such as this 5.5 quart.
  3. To a high speed blender, place 1 cup of cooled roasted butternut squash (see notes below), the soaked cashews, lemon juice, water, truffle oil, salt, nutritional yeast, cayenne pepper, and paprika. Process until smooth and creamy.
  4. Stir in the butternut squash sauce and stir until well combined.
  5. Place the homemade macaroni and cheese to a large casserole dish and top with shredded organic sharp cheddar. Put in the oven and bake for about 10-15 minutes. If you want the cheese to crisp on top, place under a broiler on LOW for 3-5 minutes. Watch closely to not burn
  6. Serve warm.

Last Step! If you loved our recipe, leave us a review below. This helps future recipe makers and ensures continued high-quality recipes for years to come!



  1. Preheat oven to 400 degrees. Cut the butternut squash in half and place a baking sheet, cut side up. Rub the flesh with extra virgin olive oil and season with salt.
  2. Roast the butternut squash for about 35-40 minutes or until flesh is fork-tender.
  3. Remove from oven and set aside to cool. When cool enough to handle, scoop out 1 cup of pulp and set aside. Reserve leftover roasted squash for another dish, double this recipe or eat it as-is!

© 2024 clean cuisine Recipe by:

Add a Salad to your Macaroni and Cheese Recipe

Greens are jam-packed with all sorts of vitamins, minerals, antioxidants and phytonutrients. The phytonutrients are what protect the plant but they also protect the plant-eater. They support a healthy immune system, reducing inflammation, etc.

Calorie for calorie, dark leafy greens deliver the most abundant, broadest spectrum of nutrients of just about any other food. For example, did you know dark leafy greens contain hefty doses of calcium, iron, potassium and magnesium?

caesar salad dressing recipe

I know how difficult it can be to introduce raw dark leafy greens to kids. But, you can always choose mild-tasting raw greens, like romaine lettuce, are very kid-friendly. Just as long as you dress it with a yummy dressing!

Making your own salad dressing is incredibly easy and SO well worth it! Check out my this omega-3 rich Caesar salad dressing before but it’s such a hit, I just had to post it again. Although romaine is the traditional lettuce served with Caesar, feel free to serve it with any green you like.

A simple chopped fresh salad with a healthy dressing is one of the easiest and healthiest ways to get your kids to eat their greens.

Choose From this List of Healthy Greens!

And, in case you’re wondering, here’s how salad greens rank, from most nutritious to least. Spinach leaves, arugula, watercress, endive, romaine, Bibb, Boston, and iceberg—basically, the darker the green the better. Have fun and enjoy!

Aimee Niedosik

Aimee loves to craft delicious, nutrient-dense recipes to share with her family and friends. While in remission from autoimmune diseases and underlying viruses, she still maintains an anti-inflammatory and anti-aging diet. Aimee is a Christian, website designer, autoimmune community leader and lives in North Carolina with her husband, 2 kids and 2 dogs.

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Friday 20th of January 2023

Great tasting cheese and macaroni. I cubed the squash before roasting. I used chickpea rotini. I really love your recipe. I've tried others and been disappointed. I served it with steamed broccoli and gluten free cornbread. Thank you for this delicious recipe. ?

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