Dairy Free Macaroni & Cheese

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When I gave up dairy it was very difficult for me to also give up my macaroni and cheese. Well… okay, honestly it was hard to give up cow’s milk dairy cheese in general. There is something to be said about the distinct flavors of Gorgonzola, creamy Havarti or a sharp cheddar, and it is very difficult to replace them. I’ve tried just about every vegan cheese out there, but it’s just not the same (and they don’t make my tummy feel very good).

But macaroni and cheese? I’ve been eating it for as long as I can remember. And I really don’t think it matters what age you are – young, old, or a thirty-something stay at home mom like me; macaroni & cheese is comfort food. Always has been, always will be. I was determined to find a dairy free replacement. Years ago I first made dairy free cheese sauce out of raw cashews. It very good, but cashews are expensive, not to mention they are very high in fat. Now don’t get me wrong, I’m not generally one to count calories or fat content (especially healthy fats), but 2 cups of cashews to 4-5 cups of cheese sauce is a little… lush. 

I wanted to create a healthier dairy free cheese sauce that was made from ingredients I already had in my pantry, was creamy, froze well, and satisfied not only me, but my children. It took a while to get the recipe just right, but once I did everyone was in agreement – they really loved this recipe for Dairy Free Macaroni & Cheese. We hope you do, too. 


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Dairy Free Macaroni & Cheese
Serves: about 4 servings
  • 12 ounces gluten free noodles (macaroni, spirals, shapes, etc...)
  • 2 cups Vegan Cheese Sauce (recipe below)
  1. Cook the noodles according to package directions. Strain.
  2. Place the noodles in a large mixing bowl and pour the Vegan Cheese Sauce over the noodles and gently stir to coat.
  3. Serve immediately.
Recipe Notes from Megan
I prefer Field Day Organic Gluten Free Pastas (locally, they are sold at Three Bears), but Tinkyada or Jovial is also good.

Vegan Cheese Sauce
Serves: about 4 cups
  1. In a high-powered blender, process the almonds or sunflower seeds into flour.
  2. Add the hemp seeds and water, and blend for 30 seconds on high.
  3. Add the nutritional yeast, garlic powder, onion powder, sea salt, Dijon mustard, lemon juice, and butternut squash, and blend until smooth and creamy.
  4. To finish the sauce, add the ghee or vegan butter substitute and blend on medium for another 10 seconds.
  5. Store in an airtight container in the refrigerator and consume within 3-5 days. Or freeze in an airtight container and consume within 6-8 weeks.
Recipe Notes from Megan
You can use this sauce immediately; however, I recommend letting it sit in the refrigerator overnight to allow the flavors to merry. The flavors will be milder on the second day, and I prefer its flavor then.

I sometimes freeze a portion of this sauce in covered ice cube trays. When my girls need an added "incentive" to eat their veggies I can easily pull out a cube and defrost it in the microwave or on the stove top.

This recipe is linked to Mostly Homemade Monday, Natural Living Monday, Teach Me Tuesday, Healthy Tuesday, Fat Tuesday, Allergy Free Wednesday, Gluten Free WednesdaysFrugal Day Sustainable Ways, Thank Your Body Thursday, Tasty Traditions, Full Plate Thursday, Simple Lives Thursday, Pennywise Platter, Healing with Food Friday, Wellness Weekend, The Paleo Rodeo and Gluten Free Fridays. 

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  1. says

    What a fantastic sauce Megan – I’ve been using butternut squash in all sorts of things recently and what a fantastic addition to this sauce! Yum!

  2. says

    WOW! Megan, this I would be willing to try, and so would my husband. We did try so much out there, and tried what was supposed to be artisan vegan cheese based on recommendations, and it just didn’t agree with us and also was not very good. I have been using frozen winter squash more since we had a lot to use from our CSA. It lends a richness that you can’t quite put your finger on. I hadn’t thought of mac ‘n cheese.

    I have read a few articles on milk casein and have discovered my husband can tolerate quite well small quantities of of raw goat and sheep cheese. Not like the huge quantities of cheese he ate before, but small quantities.



  3. says

    Hi Megan,

    Looooove mac & cheese. And I’m a ex-cheese-a-holic girl, so I here ya. I can attest for how good your recipe is, as I make a similar version, although I tend to put about a cup of Daiya cheese with the squash or cashew cream – my kiddos like the way Daiya tastes, but it is nice to not rely on packaged foods when possible (the yeast does a good job with that). Love those pretty little bacon bits on top too. :-)

  4. Selina says

    This looks amazing! Do you know how much flour 1/4 c raw almonds makes? I was thinking of making this with the almond flour I have in the pantry, plus I don’t have a food processor.

    Looking forward to making this!!

    • Megan says

      Hi Kathryn,
      I would try leaving out the hemp seeds and not substituting more sunflower seeds to begin with. Then taste it and add additional sunflower seeds if you think it needs it. I like adding the hemp seeds, not only for nutritional value, but for added creaminess. They also do a good job of balancing out the flavors in the sauce. 😉 Hope that helps!

  5. says

    Hi Megan,

    We need to eliminate many things in our household due to allergies and sensitivities. This includes gluten, dairy, eggs, yeast and sugar. It’s going to be a challenge, but thanks to people like you who are sharing their journeys it will be a little bit easier. What role does the nutritional yeast play in this recipe? Is it something that could be omitted? If you could point us in the direction of other recipes that meet our needs that would be awesome. Thanks so much!

    • Megan says

      The nutritional yeast is the flavor “backbone” of this recipe; it’s what gives it a “cheesy” flavor. Unfortunately, I wouldn’t recommend making it without it. Have you tried Daiya Cheese yet? It’s GF, DF, soy free… If that’s something you can eat, you can easily make your own homemade mac’n cheese using it. Hope that helps!!

  6. Michelle says

    Hi Megan,

    I was wondering which gluten free pasta you use? I also have multiple allergies and have noticed that most gluten free pastas have corn, or other starches in them. Thanks!


    • Megan says

      Hi Michelle,
      I normally use Tinkyada (I under cook this brand by 2-3 minutes to prevent it from getting mushy), or my favorite is Field Day Organic (which I buy locally). Both brands are only made from brown rice. 😉 Hope that helps!

  7. says

    I made this last night. Unfortunately, my memory was off on how much frozen butternut squash I had….so the sauce was 1/3 butternut squash and 2/3 pumpkin after some freezer scrounging. Still turned out amazing, but I’m hoping to make it to recipe next time to compare!! My husband raved about it, so we’ll definitely keep this in our rotation!


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