Embarking on a healthy journey doesn’t mean you have to give up your favorite comfort foods. You just need to get creative with the ingredients. This Healthy Low Fat High Protein Creamy Mac and Cheese recipe requires one pot and a 30-second butter-and-flour base. No fussy roux, no standing at the stove whisking. This is a healthier mac you’ll make again and again.
Tools I Love for This Recipe
- If you want to bake this in the oven instead, a cast-iron skillet works great. Cast-iron skillets are perfectly safe to use in the oven and under the broiler. This Lodge Cast-iron Skillet is affordable and my favorite.
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Healthy Low Fat High Protein Creamy Mac and Cheese Tips
What I love most about this recipe is that you don’t need strange ingredients like cottage cheese or additional tools like a food processor to blend in some kind of secret ingredient. You just need the cooked pasta (I recommend a high-protein pasta. I love Barilla Plus. Use cheese, milk, water and some Greek Yogurt for that perfect creamy sauce. You also only need one pan (unless you like a crispy top and choose to bake it).
The butter-and-flour base in this recipe is minimal because the Greek yogurt provides thickness as well as protein!
Make sure that you under-cook the noodles a bit. They will soak in the cheese sauce and cook more, especially if you choose to bake it! I like a sharp cheddar cheese, but you can use whatever you like! If you like a milder flavor, use monterey jack.
Just make sure you choose a good melting cheese like gruyere, fontina or gouda and do remember that it will change the calorie and fat content of the recipe. This is not the place for parmesan cheese as it will not melt like the others will.

Mac and Cheese Recipe Substitutions
I have not tested this recipe with unsweetened almond milk or any dairy-free milk. There are plenty of vegan mac and cheese recipes out there, if that is what you’re looking for!
I do not recommend gluten free pastas unless you have experience with the brand and know it will hold up to the 12 minute cook time.
I do not recommend that you try and sub in skim milk for the 2%. You need the creamier milk so your cheese sauce won’t be gritty or have an off texture. Alternatively whole milk will work just fine as its extra fat content would lend well to the sauce. Just keep in mind that you will not have the same nutritional content.
I do not use traditional elbow macaroni here because I find that cuts that are similar to penne and rotini just work better with this method.
DO NOT substitute pre-shredded cheese for freshly grated. Pre-shredded cheese has stabilizers that will change the texture of your cheese sauce!
Can I bake stove top mac and cheese?
This recipe as-written is the healthier alternative to that blue box we all grew up with. If you want to bake this recipe, it’s very easy. Just get out a baking dish that is safe under a broiler and spray it with cooking spray. I love using my 10-inch cast iron skillet for this.
Preheat your broiler and pour the mac and cheese into the dish. Top it with panko bread crumbs crackers or simply some extra shredded cheddar and place it under the broiler for 2.5 minutes.
Storing Leftovers
Your leftovers can be stored in an airtight container for 3-4 days. I don’t recommend freezing this recipe as anything with dairy doesn’t freeze well.

Your Favorite Comfort Food Made Over
I love making over my favorite comfort foods, but I’ll never change them so much that you need to use your imagination to convince yourself it’s the traditional recipe. Mac and cheese is the ultimate comfort food and this is low calorie mac and cheese in the sense that it’s a fraction of what your traditional recipes would be.
This recipe is one that your picky eaters are not going to turn their nose up. This is a great way to get everyone on-board with healthier choices. Notice I said healthier- not perfect!
Pin for Later!
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My Gluten Free Chinese Lo Mein is another cozy noodle night.
My Vegan Street Taco with Crispy Tofu is a fun meatless night.
You might also love my Crispy Pan Fried Tofu.

Healthy Low Fat High Protein Creamy Mac and Cheese
Ingredients
- 8 ounces Barilla Plus Penne Pasta Or another high protein pasta of your choosing
- 1 tbsp butter
- 1 tbsp flour
- 5 ounces Nonfat Greek yogurt
- 1 cup Fairlife 2% milk
- 4 ounces Shredded Sharp Cheddar
- 1 tsp. salt
- 1/2 tsp. pepper
Instructions
- Boil Pasta according to package instructions for al dente. You want to leave a little bite in the pasta. Drain Pasta and Set aside. Set your pan back over low heat and melt the butter and flour together. Stir for about 30 seconds.8 ounces Barilla Plus Penne Pasta, 1 tbsp butter, 1 tbsp flour
- Pour in the milk and allow the sauce to thicken. Add in salt and pepper once thickened (thickening over medium low heat should take about 5 minutes) Whisk in the Greek Yogurt.5 ounces Nonfat Greek yogurt, 1 cup Fairlife 2% milk, 1 tsp. salt, 1/2 tsp. pepper
- Move the pasta off of the heat and stir in the cheeses. Season with more salt and pepper to taste. Add a little more milk 2 tbsp. at a time if you need to thin it out as this mixture will thicken as it sets.You can also bake this mac and cheese. Simply add some panko bread crumbs and broil for about 3-5 minutes or until bubbly and delicious. Note that this will thicken it more and give it that baked macaroni and cheese texture.4 ounces Shredded Sharp Cheddar


Meche
Sunday 2nd of June 2024
Cheese didn’t mix in with pasta 🥲
Krysten
Monday 3rd of June 2024
I'm sorry you had trouble with this recipe, it would definitely seem the quality of the cheese is a factor and it must not be pre-shredded which has stabilizers in it. I am retesting this one as a few readers have said this while others have great success.
Thank you!
Paul
Tuesday 21st of May 2024
This was a very delicious and quick and easy. I did use packaged non-dairy cheese Daiya Cheddar and Italian Blend. The cheese melted perfectly and still had the texture and flavor of dairy cheese. May add some tomatoes and spinach for an even healthier meal. Will definitely be making this again.
Krysten
Thursday 23rd of May 2024
Awesome! I am so happy to hear that! :)
Colby
Friday 22nd of March 2024
I don’t understand! Followed the recipe, but when I combined the cheeses with the pasta and water/milk mixture, the cheese did NOT mix in with it all. It just chunked up. Nothing melted together. I shredded the cheese myself, did not buy pre-shredded.
Krysten
Monday 25th of March 2024
Interesting- did you stir the cheese in at the end - and off of the heat? I have not had that problem before however if you had too hot, it may have wanted to clump together.
Francesco Gatti
Friday 8th of November 2019
Macaroni and cheese, it’s my all-time favorite recipe. And it's looking so much delicious with lots of cheese and creamy texture. Those points and notes you have mentioned in this article are very useful. Thank you so much for this lovely recipe.
Krysten
Friday 8th of November 2019
You're welcome! :) Hope you love it!