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I scoured the web for the tastiest-looking (4.5-5 star) homemade mac and cheese recipes and I changed them to use healthier ingredients.

homemade mac and cheese recipes
Image source: Google

Healthier homemade mac and cheese

Updated: October 17, 2019

*Healthier versions of mac and cheese – made with spelt pasta, sprouted whole wheat flour and no cow’s milk.*

Well, kids love Kraft Dinner. Didn’t everyone grow up with Kraft Dinner? I know I did, and I loved it too. But, as I’m sure everyone now knows, processed and/or packaged food are not healthy choices. Whole foods are the way to go. Besides, homemade (healthy) mac and cheese tastes so much better anyway.

Healthier ingredients

These recipes are made with unsweetened coconut milk but, trust me, you can’t taste the coconut, it’s very mild. I use every time I bake or cook.

I suggest using goat cheese which is much easier to digest than cheese made with cow’s milk, because it doesn’t contain the A2 casein that many people cannot tolerate.

I also suggest using sprouted wheat which is easier to digest than modern wheat, it’s healthier for you and it’s a great substitution for those who can’t tolerate modern (durum) wheat, which is why I recommend using almond flour as well (to replace bread crumbs). Read more about sprouted wheat HERE.

Homemade mac and cheese recipes

I scoured the web for the tastiest-looking (and most with 4.5-5 star ratings) homemade mac and cheese recipes and I tweaked them to make them healthier.

I recommend adding veggies (broccoli is great) for an even healthier meal. Enjoy!

1. Easy stove-top mac and cheese

Recipe adapted from Genius Kitchen.

Homemade Mac and Cheese

Genius Kitchen



  1. Cook pasta according to package directions.
  2. In medium saucepan, melt ghee over medium heat; stir in flour, and cook for 3-5 minutes to form a roux; add salt and pepper; slowly add milk, stirring well after each addition.
  3. Cook and stir until bubbly.
  4. Stir in cheese, a small amount at a time until fully melted.
  5. Drain pasta; add to cheese sauce; stir to coat.

See original recipe HERE.

2. Baked mac and cheese

Recipe adapted from Recipe Tin Eats.

homemade mac and cheese

Recipe Tin Eats



  • 8 oz spelt pasta or quinoa pasta (or other healthier option)
  • 1 tbsp ghee (grass-fed if possible)



Seasonings (optional):

  • 1 tsp organic garlic powder
  • ½ tsp organic onion powder
  • ½ tsp organic mustard powder (optional)


For the pasta:

  1. Bring a large pot of water to boil. Add macaroni and cook per packet directions MINUS 1 minute.
  2. Drain, return pasta to pot, add ghee and toss until melted. Set aside to cool while making the sauce (optional – note 1).

For the topping:

  1. Mix together topping. Set aside.

For the sauce (this video is helpful):

  1. Preheat oven to 350 dF.
  2. In a large saucepan or in an ovenproof skillet, melt ghee over medium heat. Add flour and cook, stirring constantly, for 1 minute.
  3. Add about 1 c of the milk and mix to dissolve the paste into the milk. Then add remaining milk and mix until lump free (use whisk if required).
  4. Mix in salt and seasonings, if using.
  5. Cook, stir/whisk regularly, for 5 – 8 minutes until thickened to a cream consistency. When the sauce coats the back of a wooden spoon, you should be able to draw a path with your finger.
  6. Remove from stove, add cheese and stir – cheese doesn’t need to melt.
  7. Adjust salt to taste.


  1. Pour sauce into pot with pasta. Stir quickly, then pour back into the skillet or a baking dish. Sprinkle with almond flour ‘breadcrumb’ topping.
  2. Bake for 25 minutes or until top is light golden. Don’t bake too long otherwise you’ll bake away the sauce!
  3. Serve immediately!


  1. Tossing the cooked pasta with butter provides a light coating that helps prevent it from bloating while baking in the sauce. This is also the reason why I let the pasta cool before mixing in with the sauce. You could just make the sauce while the pasta is cooking.
  2. MAKE AHEAD: Homemade mac and cheese is best made fresh but if you need to make ahead, this is the best way. Cook pasta and toss in ghee, cool. Make cheese sauce per recipe, then cool with LID ON (important, to avoid evaporation). Make topping. Store all components separately in the fridge until required. Mix sauce and pasta, top with topping then bake per recipe.
  3. REHEATING: Homemade mac and cheese is best served fresh. But if you can’t do that,  take it out of the oven as soon as the top is light golden at about 20 minutes. Then it will be saucier than cooking for the full time which is fine. Cool completely uncovered, then cover in beeswax wrap or silicone bowl covers and refrigerate. Remove from fridge 30 minutes before reheating. 

See original recipe HERE.

3. Perfect creamy macaroni and cheese

Recipe adapted from Seasons and Suppers.

homemade mac and cheese

Seasons and Suppers


  • 8 oz spelt pasta
  • 1/4 cup ghee (grass-fed if possible)
  • 1/3 cup sprouted whole wheat flour
  • 3 cups coconut milk
  • 10 oz goat cheese, grated
  • 1/2 – 1 tsp celtic sea salt (1/2 tsp if using table salt)
  • 1/4 tsp organic chili powder (optional)
  • 1/8 tsp organic garlic powder
  • 1/2 oz additional goat cheese, grated
  • 1/4 tsp organic chipotle chili powder (optional)


  1. Add water and a bit of salt to a large pot and place over high heat for the pasta. While it’s heating, prepare the cheese sauce.
  2. For the cheese sauce:
  3. In a large saucepan, melt the ghee over medium heat. Whisk in the flour and continue to whisk and cook for about 2 minutes.
  4. Very slowly add the milk, a little at a time, whisking constantly. Once all the milk has been added, cook, stirring frequently until the sauce thickens, about 10 minutes. (Don’t rush this step. The mixture will not be thick, but will noticeably thicken after 8-10 minutes of cooking).
  5. Remove saucepan from heat. Add the cheese, salt, chili powder and garlic powder. Stir until the cheese is melted and all the ingredients are incorporated, about 3 minutes. (If the cheese isn’t melted completely after about 3 minutes, you can put the pan back on low heat and stir until it is melted). Set aside for a minute.
  6. Preheat oven to 350° with rack in the centre of the oven. Grease an 8-inch square baking dish, an 8-inch cast-iron skillet or individual baking dishes.
  7. When the water is boiling, add the pasta and cook for 2 minutes less than the package directions indicate. (The noodles will finish cooking in the sauce in the oven). When the pasta is cooked, drain and immediately rinse well with cold water. Make sure your pasta is well-drained.
  8. Add the cooked pasta and to the cheese sauce and mix gently, but thoroughly. (It might look like too much sauce or too little pasta, but trust me, it will all be good in the end). Spoon or ladle the mixture into a prepared baking dish or individual dishes. Sprinkle the top of each with a bit of additional grated cheese (you don’t need a lot here, as there is plenty in the sauce), then sprinkle with the chipotle chili powder.
  9. Bake in the preheated 350° oven uncovered for 20 to 25 minutes, until the sauce has bubbled up around the edges and the top has a nice golden crust. Let sit for a few minutes before serving.

See original recipe HERE.

4. Family favorite baked mac and cheese

Recipe adapted from The Chunky Chef.

homemade mac and cheese



  1. Preheat oven to 325 degrees F and grease a 3 qt baking dish (9×13″).  Set aside.
  2. Bring a large pot of salted water to a boil.  When boiling, add pasta and cook for 1 minute less than the package directs for al dente.  Drain and drizzle with a little bit of olive oil to keep from sticking.
  3. While water is coming up to a boil, grate cheese and divide into three sections.  Approximately 1 cup for the sauce, 3/4 cup for the layer, and 3/4 cup for the topping.
  4. Melt ghee in a large saucepan over medium heat. Sprinkle in flour and whisk to combine.  Mixture will look like very wet sand.  Cook for approximately 1 minute, whisking often. Slowly pour in about 1 cup or so of the milk, while whisking constantly, until smooth.  Slowly pour in the remaining milk, while whisking constantly, until combined and smooth.
  5. Continue to heat over MED heat, whisking very often, until thickened to a very thick consistency.  It should almost be the consistency of a semi thinned out condensed soup.
  6. Stir in spices and half the cheese, stirring to melt and combine. Stir in remaining cheese, and stir until completely melted and smooth.
  7. In a large mixing bowl, combine drained pasta with cheese sauce, stirring to combine fully.  Pour half of the pasta mixture into the prepared baking dish. Top with reserved layer grated cheese, then top that with the remaining pasta mixture.
  8. Sprinkle the top with the topping grated cheese and bake for 15 minutes, until cheesy is bubbly and lightly golden brown.


Mac and cheese can be made ahead:

  • Make as directed (but do not bake), transfer to baking dish and cool completely.  Cover tightly with beeswax wrap or silicone bowl covers and refrigerate 1-2 days ahead.  
  • Before baking, let dish sit on counter for 30 minutes.
  • Bake at recipe temperature for 25-35 minutes, until hot and bubbly.  

I cut this recipe in half. See original recipe HERE.

5. Best stove-top mac and cheese

Recipe adapted from Gimme Some Oven.

homemade mac and cheese

Gimme Some Oven


  • 1 tbsp ghee (grass-fed if possible)
  • 1 tbsp sprouted whole wheat flour
  • 1 1/2 cups water
  • 2 cups coconut milk
  • 1/2 pound spelt pasta
  • 1/2 – 1 tsp celtic sea salt
  • 1/4 tsp organic garlic powder
  • 1/8 tsp organic ground mustard
  • 2-3 cups freshly-grated* goat cheese
  • 1/4 cup Go Veggie parmesan cheese


  1. Melt ghee in a large stockpot over medium-high heat.  Add flour, and stir until combined.  Cook for 1 minute, stirring occasionally.  Then pour in 1/2 cup of the water, and stir (or whisk) until the mixture is completely smooth and begins to thicken.  Gradually pour in the remaining water and milk, stirring until evenly combined.
  2. Stir in the pasta, salt, garlic powder, and mustard until combined. Then continue cooking, stirring occasionally, until the mixture just reaches a simmer. *I recommend grating your cheese while the pasta cooks to save time! Reduce heat to medium-low to maintain the low simmer. Continue cooking, stirring occasionally, for about 9-10 minutes, or until the pasta is al dente. Be careful not to overcook the pasta!
  3. Remove from heat, and stir in the cheeses until melted.  Taste, and season with additional salt (and black pepper, if you’d like), as needed.
  4. Serve immediately, and enjoy!

*Be sure to always purchase block cheeses for this recipe, and then grate/shred them at home.  Store-bought shredded cheeses usually have a coating on them (to prevent them from clumping) which prevents them from melting smoothly.  I know it’s a bit of extra work, but it’s worth it to shred them yourself…which I recommend multi-tasking while the pasta is cooking.

I cut this recipe in half. See original recipe HERE.

Please share if you know someone who would love these recipes. Thanks! 🙂

Do you have a deliciously healthy homemade mac and cheese recipe? Which homemade mac and cheese recipes have you tried? Share your comments below.

I wish you health and happiness,


A round up of five healthier homemade mac and cheese recipes (paleo, gluten-free and veggie crusts).

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