Greek Yogurt Mac and Cheese

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Gluten-Free Baked Greek Yogurt Mac and Cheese is an easy, healthier version of everyone’s favorite comfort food! It’s gluten-free and protein-packed and a great make-ahead dish to feed a crowd!

Side view of a baking dish of Greek Yogurt Mac and Cheese

I have four kids (and a husband who has the tastebuds of an eight year old boy). So it should come as no surprise to you that we eat a lot of macaroni & cheese around here.

I’m a firm believer that making homemade versions of your favorite pre-packaged foods is always a better choice! Knowing exactly what is in the food I feed to my family is extremely important to me. 

Since nutritious eating can (and should) include our favorite foods…I’d like to think this Greek Yogurt Mac and Cheese is healthy comfort food at it’s finest!  You really can’t beat a dish that is gluten-free, loaded with protein and beloved by both kids and husbands with kid-like tastebuds!

This healthy mac and cheese recipe is my oldest daughter’s favorite dinner. She often very 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 healthy mac and cheese 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}!

Overhead view of a rectangular baking dish of gluten free Greek Yogurt Mac and Cheese with parsley sprinkled on top

How to make Greek Yogurt Mac and Cheese

This dish is just as easy to make as it is to get your kids to eat it! 😉

1. Rinse Pasta Well with Cold Water

After cooking the pasta be sure to drain it and rinse it well with cold water. This ensure that the heat the noodles give off as they cool won’t cause it to become over cooked!

overhead view of a baking dish with noodles before the cheese sauce is added to this gluten-free Greek Yogurt Mac and Cheese

2. Whisk!

When you make the sauce,  be sure to whisk in each ingredient until the mixture is homogenous and smooth.

3. Make-Ahead!

This Greek Yogurt Macaroni & Cheese can be made ahead of time and baked when you’re ready. Just assemble and leave it covered at room temperature (for up to one hour) or in the refrigerator! If the dish is cold when you put it in the oven, be sure to cover it with foil for the first 10 minutes of baking! This will ensure that the inside gets warm before the top browns!

Overhead view of a baking dish with gluten free Greek Yogurt Mac and Cheese before it's put in the oven

4. This Greek Yogurt Mac and Cheese can be made on the stovetop! (No Baking)

You do not have to bake this recipe either! It can easily be converted to a stovetop  Greek Yogurt Macaroni & Cheese by simply not making the toping and skipping the baking! However, I think the crispy, cheesy, flavorful top layer is a non-negotiable part of this dish {and so does Bethany}! 😉

Baking dish of greek yogurt mac and cheese with a spoon in it

Greek Yogurt Mac and Cheese: Substitutions 

I have made this recipe so. many. times! I guarantee you will have the best outcome if you follow it as written! However, there are a few acceptable substitutions you can make and still get delicious results!

  • Gluten-free Pasta: 8 oz of any pasta variety can be used in this dish whether they contain gluten or not. The possibilities are endless, just be sure to use a variety that complies with your dietary needs.
  • Tapioca flour: Arrowroot powder, cornstarch or all-purpose gluten-free flour can be used in place of tapioca flour. If you do not need to make a gluten-free version then regular, all-purpose flour works well too!
  • 2% Milk: Whole milk can be used in place of 2%!  I do not recommend skim milk because your final product won’t have the dreamy creaminess that makes this recipe so good!
  • Plain Greek Yogurt: I have used all different kids of plain Greek yogurt {including fat-free} with great results!
  • Cheddar Cheese: Use your favorite variety and sharpness of cheese! My family likes medium cheddar cheese the best, however I am a firm believer in the sharper the better! 😉 I have even used half mozzarella in a pinch and it still turns out great!
Baking dish with greek yogurt mac and cheese with a scoop being taken out with a wooden spoon

More delicious mac and cheese recipes: 


Greek Yogurt Mac and Cheese

Gluten-Free Baked Greek Yogurt Mac and Cheese is an easy, healthier version of everyone’s favorite comfort food! It’s gluten-free and protein-packed and a great make-ahead dish to feed a crowd! 
5 from 7 votes
Course Main Course, Side Dish
Cuisine American
Servings 10 Servings
Calories 367
Prep Time10 minutes
Cook Time20 minutes
Total Time30 minutes


Macaroni and Cheese:



  • 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!


Calories: 367kcal | Carbohydrates: 43.8g | Protein: 15g | Fat: 16g | Cholesterol: 3mg | Potassium: 21mg | 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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Recipe Rating


  1. 5 stars
    Thank you for the recipe. It was so good! My husband who is a picky eater went back for a second helping! I will definitely make it again!