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. Do you think this would be good made a day in advance? I was thinking of making ahead and just waiting to do the topping and baking the day of.

  2. 5 stars
    This sounds like a winner. I will give it the “Hitchcock Test” and see if Katie, Christina and Emily will be able to taste the difference.