Healthy Greek Yogurt Mac and Cheese (Gluten-Free)!

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Today I have a healthier mac and cheese recipe for you. This Healthy Greek Yogurt Mac & Cheese is loaded with protein, gluten-free (but can be made gluten-full too), and tastes absolutely amazing.

This Healthy Mac & Cheese recipe is gluten-free and loaded with protein! A quick & easy, healthy dinner recipe that your whole family will love!


This Healthy Greek Yogurt Mac & Cheese is made more nutritious by using Greek yogurt in place of most of the butter. The richness and flavor of the yogurt also means we can use 2% milk instead of whole milk or cream without losing any of the creamy, comforting, cheesy goodness.

This Greek Yogurt Macaroni & Cheese is my oldest daughter’s favorite dinner. She often specifically requests, “the mac & cheese with the stuff on top that you make, not the box.” Since there is an entire cup of Greek yogurt in this recipe it’s a great source of protein, so I usually serve it as a meatless main dish. You could easily serve it as a side or a make-ahead lunch (because it makes amazing leftovers).

Even though my family doesn’t follow a specific diet, I love taking recipes we always eat and making them gluten-free. That way, when friends or family who have dietary restrictions come over for dinner, I already have a repertoire of recipes I can choose from without having to create something new at the last minute.

This Healthy Mac & Cheese recipe is gluten-free and loaded with protein! So much better than the beloved blue-box!

Healthy Greek Yogurt Mac & Cheese: Ingredients & Substitutions

  • Flour: I have made this dish using tapioca flour for a gluten-free option, but you may use regular all-purpose flour if you don’t eat a strictly gluten-free diet.

How to Make Healthy Greek Yogurt Mac & Cheese

I have some step-by step photos for you to show how to make this Healthy Greek Yogurt Mac & Cheese in action. Start by making the cheese sauce from butter (only 2 TBS!), tapioca flour, milk and yogurt. Then add more yogurt, cheese and some other deliciousness to finish it off.

This Healthy Mac & Cheese recipe is gluten-free and loaded with protein! So much better than the beloved blue-box!

Once the sauce is finished, add it to the already cooked macaroni. Choose your favorite variety that complies with your lifestyle. I love these Ancient Harvest Quinoa Pasta Elbows for a gluten-free option. It’s one of my favorite gluten-free pasta varieties because it uses quinoa which increases the protein content of the dish. You can also use regular-old macaroni. You technically could stop at this step and serve it stove-top style…

This Healthy Mac & Cheese recipe is gluten-free and loaded with protein! So much better than the beloved blue-box!

…but I’m all about the crispy, cheesy, flavorful top layer that is created when this Healthy Greek Yogurt Mac & Cheese is baked. Spread the noodles & cheese mixture in a 9″ baking pan and sprinkle the top with parmesan cheese, almond meal, garlic salt and pepper. Then pop it in the oven for 20-30 minutes until it’s golden brown and bubbly…

This Healthy Mac & Cheese recipe is gluten-free and loaded with protein! So much better than the beloved blue-box!

…and presto. You have a delicious baked mac ‘n cheese that is healthy and kid-approved!

Recipe FAQs

Can I use Greek yogurt instead of milk in mac and cheese?

Yes! It creates a creamy consistency.

Does this recipe have to be gluten-free?

No, feel free to use any flour if you don’t need it to be gluten-free.

Is mac and cheese a side dish?

Mac and Cheese can be either a side dish or main dish. This recipe has more protein in it which makes it a great main dish.

More Delicious Recipes

This Healthy Mac & Cheese recipe is gluten-free and loaded with protein! So much better than the beloved blue-box!

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Baked Greek Yogurt Mac and Cheese

Laura
This Healthy Greek Yogurt Mac and Cheese is the perfect weeknight meal loved by kids and adults! 
5 from 6 votes
Course Main Course, Side Dish
Cuisine American
Servings 10 servings
Calories 367
Prep Time10 minutes
Cook Time20 minutes
Total Time30 minutes

Ingredients 
 

Topping:

Instructions 

  • Preheat oven to 375 degrees F. Grease an 8×8” baking dish (or 2 quart casserole dish), set aside.
  • Cook pasta according to package instructions.
  • Drain and rinse pasta with cold water, transfer to a large bowl and set aside.
  • Measure out dry ingredients (tapioca flour, onion powder, garlic powder, salt and pepper) into a small bowl. Set aside.
  • Add butter to a medium saucepan. Heat over medium heat until melted.
  • Once butter is melted, add dry ingredients and whisk until combined.
  • Cook on medium-high heat for 30 seconds or until it forms a paste-like consistency and becomes light brown.
  • Add milk and whisk until ingredients are combined.
  • Add Greek yogurt and whisk until combined.
  • Cook the mixture over medium-high heat until it begins to thicken (but does not boil).
  • Once the mixture is thick, turn heat to low and add 2 cups of cheese. Stir until the cheese is melted.
  • Add cheese sauce to the cooked and drained pasta and stir to combine.
  • Pour mixture into prepared baking dish.
  • In a small bowl, combine topping ingredients.
  • Sprinkle topping over pasta.
  • Bake in preheated oven for 15-20 minutes or until the cheese on the top is melted and slightly browned.
  • Serve warm!

Notes

Ingredient Substitutions 

I have made this dish using tapioca flour for a gluten-free option, but you may use regular all-purpose flour if you don’t eat a strictly gluten-free diet.

Storage

Keep in the fridge in an air-tight container for up to 3 days or freeze for up to 2 months. 

Nutrition

Calories: 367kcal | Carbohydrates: 43.8g | Protein: 15g | Fat: 16g | Cholesterol: 3mg | Potassium: 146mg | Fiber: 4.6g | Sugar: 4.2g | Calcium: 90mg | Iron: 2.7mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Did you enjoy this recipe? Have a question? Leave a comment below!

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24 Comments

  1. Your Greek Yogurt Mac and Cheese looks wonderful, thanks so much for sharing with us at Full Plate Thursday!
    Miz Helen

  2. I love this idea! and it’s a great healthy alternative to a classic too, I love greek yoghurt in general so I can’t wait to try this new twist and see how it tastes! Thanks for linking to #YumTum this week

  3. Oh this sounds good and I love the fact that you used greek yogurt! Thanks for sharing at Thursday Favorite Things!

  4. Healthy mac and cheese? I’ve never heard of such! This sounds so good, I can’t wait to try it. Pinning! Thanks for sharing at Inspiration Thursday.

  5. Oh my gosh, this looks absolutely unreal!! Any sort of cheese sauce… YES PLEASE! I love that it’s lightened up but doesn’t sacrifice flavor for health :).

  6. This looks delicious! I love the idea of using yogurt and will have to give it a try. Thank you for joining the Link-Up. Pinned Yummed 🙂

  7. 5 stars
    Sadly I also love hot dogs in my mac & cheese ???????? … I’ll let you know how this recipe goes over with the hubs!!

    1. LOL Case! There are quality brands of hot dogs out there…we usually buy Nathan’s. I’ve never been a hot dog fan but recently I started cooking them in the oven (at 425 for like 10-15 minutes) and that’s the only way they are slightly tempting to me! There’s something about the roastedness of them after being cooked in the oven that makes me want to eat them! 😉