Clean Eating Macaroni And Cheese Recipe

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This clean eating macaroni and cheese recipe is a great way to give the kids what they want and still feel good about it!

The truth is, I’ve completely slacked off on kid recipes because Mini Chef eats so much of what I eat now. I no longer have to cook separate meals for him unless I make something spicy. But even my kid is not immune to things he sees in the stores and in other people’s homes. After all, Mac & Cheese is an American tradition. I don’t know many households that don’t have a Kraft box in their cabinets somewhere. It’s a staple, especially if you have kids in the house. And on top of that, it’s cheap!

A white bowl of Clean Eating Macaroni And Cheese is shown from the side. You can just see over the rim of the bowl to see shredded cheese melting over the pasta.

But I think most clean eaters realize that when something can sit on a shelf for years in a box, comes with powder and is for sale at 10 boxes for $1, it’s probably not the most healthy choice you could be making.

One look at the ingredient list alone is enough to send you back to kindergarten because you think you forgot how to read the English language. But the truth is, all those chemicals are not only unreadable and unpronounceable, but indigestible as well!

Now, I’ll be the first to admit that full fat cheddar cheese is not something you want to eat tons of. Not because it’s overly processed, but because of the fat content. Even though healthy fats are necessary, they still need to be enjoyed in balance and moderation.

But here’s the thing. Anyone who has kids knows how important it is for kids to “be just like their friends”. And if my child absolutely MUST have Mac & Cheese, you can bet I’ll make him this clean eating macaroni and cheese with real, full fat cheese before I go to the store for a box of powder and chemical ingredients I can’t pronounce. Am I wrong?

Besides, kids who truly have weight problems most likely have bigger issues with their overall diets than cheese. We need to get them off the sodas, chips and corn dogs!


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Clean Eating Macaroni And Cheese

Clean Eating Macaroni And Cheese

This delicious make-at-home mac and cheese is so much healthier than the boxed stuff!
Print Pin Rate
Course: Pasta
Cuisine: American
Prep Time: 10 minutes
Cook Time: 20 minutes
Total Time: 30 minutes
Servings: 2 servings
Calories: 451kcal
Author: The Gracious Pantry


  • 2 cups cooked whole grain pasta
  • 1/2 cup milk
  • 1 cup sharp cheddar cheese (shredded from a block and lightly packed for measuring)
  • 1/8 tsp. dried mustard
  • 1 tbsp. whole wheat pastry flour (affiliate link) (regular whole wheat will work, but will give a grainier texture)
  • salt to taste


  • In a medium pot, warm the milk over medium heat. You want it hot, but not boiling.
  • Whisk in the flour. Continue whisking for 2-3 minutes to be sure it's well incorporated and doesn't settle to the bottom.
  • Whisk in the mustard.
  • Remove pot from heat and stir in the cheese. Stir until completely melted and combined. If the cheese doesn't melt enough, return pot to the stove over low to medium heat.
  • VERY IMPORTANT: Do NOT let the sauce boil. You only want the pot on the heat until the cheese is just melted. Then remove immediately.
  • Add salt to taste and pour sauce over your pasta.


Please note that the nutrition data below is a ballpark figure. Exact data is not possible.


Serving: 0.5the recipe | Calories: 451kcal | Carbohydrates: 43g | Protein: 23g | Fat: 21g | Saturated Fat: 13g | Cholesterol: 65mg | Sodium: 381mg | Potassium: 219mg | Fiber: 6g | Sugar: 4g | Vitamin A: 665IU | Calcium: 496mg | Iron: 2mg

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  1. Weehamfam says:

    This is how I make my macaroni cheese, passed down a few generations, my kids LOVE IT. Freezes really well. Also good with peas and/or sweetcorn mixed through.

    1. Anonymous says:

      Weehamfam – Wonderful! Love the freezer tip. Mine didn’t last long enough to find out if it freezes or not. So thanks!

  2. Jarenb0826 says:

    YUMMY!!! Can’t wait to try this!

    1. Anonymous says:

      Jaren – Hope you enjoy it!

  3. Lydia Campos says:

    Well I am no kid but I do love a good bowl of mac and cheese. I know that my kids will love it too!

    1. Anonymous says:

      Lydia – I think we’re all kids at heart! Enjoy the mac & cheese!

  4. Anonymous says:

    Carole – Fantastic! I should say though, that if your child is used to the boxed version, it may take a little getting used to this cleaner version. But it’s yummy, and hopefully it will go over well. Let me know how it turns out!

    1. Carole Nelsen Bates says:

      I tried this for the first time Monday and you were right – she did not like it. But, I will try again! I thought it was good. I added about a T of green yogurt to it and topped it with some cayenne pepper to give it some kick. 🙂

      1. Anonymous says:

        Carole – What is green yogurt?

  5. Anonymous says:

    Naomi – Yes! He called and told me you liked it this way! LOL!

  6. Anonymous says:

    Jenn – That’s awesome!! Homemade is always better!

  7. Anonymous says:

    SFS – You’re welcome! I hope she will enjoy it!

  8. Anonymous says:

    Laurie – You can leave it out.

  9. So glad I came across this recipe! My 3 year old son loves mac and cheese(too much) and I hate giving him the kind out of the box. I will definitely be making this for him : ) Thanks!

    1. Anonymous says:

      Brittany – You’re welcome! Hope he enjoys it!

  10. Anonymous says:

    Natasha – Thanks! I’ll give that a try.

  11. Anonymous says:

    Melanie – Enjoy!

  12. Anonymous says:

    LB – Yay!! I’m so happy you all enjoyed it!

  13. Nancy Steffan says:

    I make something similar for my kids, though I don’t use whole grain pasta (yet) or whole wheat flour (yet). My mother adds in whole tomatoes from a can (with the juice) and I changed that to tomato juice (don’t like whole tomatoes). I’m going to have to try the whole grain/whole wheat route.

    My kids are always asking for grilled cheese and pizza. Do you have clean eating recipes for either? Thanks!


    1. Anonymous says:

      Nancy – The only way to clean up a grilled cheese sandwich is to use clean bread and real cheese.

      Pizza recipes I have several of here. Go to categories and scroll down to the pizza category. Hopefully you’ll find something there you like. Enjoy!

  14. Teenylittlesuperchef says:

    Gotta love some mac and cheese! I like making mine with a little bit of butternut squash puree and Greek yogurt added in. It doesn’t change the color or flavor much, but really adds a whole lot of creaminess and allows you to cut down on some of the cheese. Plus it’s a good way to sneak in more Vitamin A 🙂

    1. Anonymous says:

      TLSC – What a great tip! Thanks!

    2. oh yum, I bet the yogurt works well! may have to try that way too!

      1. graciouspantry says:

        I hope you enjoy it!

  15. Hey, not only kids love macaroni and cheese! lol I’m so glad you have a clean recipe for this. This is my absolute favorite dish to prepare and make for whenever my family has a big dinner. I’m going to try this recipe out for hubs and I on Sunday. If it turns out right, I’ll make it to bring for Thanksgiving instead of the Paula Deen version I usually make lol.

    1. Anonymous says:

      Tiffany – Wonderful! I hope you enjoy it!

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  17. Anonymous says:

    Erin – Give the kids some time. When you are used to processed foods, whole, natural foods do taste strange and have strange textures. But with time, you will all get used to it and wonder how you ever liked the other stuff.

  18. Anonymous says:

    Julie – Fabulous!! Glad it worked out!

  19. graciouspantry says:

    Gina – That’s a very interesting and valid point. When kids are used to the boxed version, it can be tough to switch them over. A new name is perfect!

  20. graciouspantry says:

    Jamie – Aaah yes. That would make sense. Blonde moment on my end. I should have figured that one out!

  21. graciouspantry says:

    Rose – You can say that again! I love my comfort foods!

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  23. graciouspantry says:

    Mommy – Wow. That’s a tough one. Let me think on that for a while…

  24. Nicole S. says:

    Just made this with whole wheat flour, added a little garlic powder, a teeny bit extra mustard and some salt and it’s DELISH! I would say the consistency is comparable to the Shells ‘n Cheese you get in the box. VERY creamy!

    1. graciouspantry says:

      Nicole – Glad you enjoyed it!

  25. graciouspantry says:

    Great! I hope you all enjoy it!

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  27. graciouspantry says:

    Heather – The flour is for thickening. You could try an organic cornstarch but not sure how that would taste. Keep in mind that if your family is used to white flour, it will take some time for their tastes to adjust. Don’t give up. Try mixing half and half until they get used to that, and then move on to completely whole wheat.

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  29. graciouspantry says:

    Fabulous! Thanks!

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  31. shelley landsburg says:

    mine is a fussy teen so I have used the pasta that is “whie” 🙁 but has fibre in it>

  32. Just threw this together for lunch. So easy and yummy! Made a few changes- used medium cheddar and no ground mustard. Thank you!

  33. Jeff Hamlin says:

    Now if only I could figure out how to convert this to slow cooker method, it would be great! 🙂

    1. The Gracious Pantry says:

      I don’t recommend it. Pasta is VERY touchy in a slow cooker.

  34. OMG! I can’t wait to try this! My kiddos love Mac & Cheese and we just started eating clean.

    1. The Gracious Pantry says:

      I hope you all enjoy it! 🙂

  35. I just made this, and I am practically licking the bowl clean! It is Soooo good!

  36. Liz Karem says:

    Do you think I can make this with almond milk? I try to avoid buying cow’s milk, but I do always have cheese around. I’d love to make this (I just finally convinced hubby that box junk was JUNK), but I don’t want to have to keep skim milk on hand. Thank you for having a recipe! (I told hubby you would!)

    1. The Gracious Pantry says:

      Liz – I haven’t tried it. In theory, it should work just fine. But almond milk can also be a little touchy when heated. So it’s a gamble. Sorry, I wish I had more info on that for you.

  37. Sounds good! 🙂 I have to admit, I love, love, love mac and cheese. I’ll have to try this (and eat a smaller portion) 🙂

    1. The Gracious Pantry says:

      Sara – Great! Let me know how you like it!

  38. WoW! so quick and easy and SO YUMMY!

    1. The Gracious Pantry says:

      Steph – Glad you enjoyed it! 🙂

  39. I made this tonight but I mixed in some organic beef, used almond milk and whole wheat flour to make if beefy mac and cheese! It was delicious!

    1. The Gracious Pantry says:

      Monica – Awesome! So glad you enjoyed it!

  40. Throw a carrot, an onion and a stick of celery in a food processor and fry it in a little oil and add to the mix if you want to veg it up a little

    1. The Gracious Pantry says:

      Yolanda – Great idea!!!

  41. Tristen Strauss says:

    I’m excited to try this recipe…I’m a bit of a mac and cheese addict. 🙂

    1. The Gracious Pantry says:

      Tristen – I hope you enjoy it! 🙂

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