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You are here: Home / Gluten-Free / Greek Yogurt Mac and Cheese

Greek Yogurt Mac and Cheese

Last updated on September 18, 2020. Originally published July 26, 2017 17 Comments

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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, β€œthe 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! πŸ˜‰

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}! πŸ˜‰

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! πŸ˜‰ 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: 

  • This homemade mac and cheese made on the stovetop is our favorite!
  • For something different (and low carb), try this spaghetti squash mac and cheese!
  • Add some nutrition and make this Vegetable Mac and Cheese!

IF YOU MAKE SOMETHING FROM JOYFOODSUNSHINE I WOULD LOVE TO SEE YOUR CREATIONS! DON’T FORGET TO RATE THIS RECIPE AND LEAVE A COMMENT BELOW! ALSO, FOLLOW ALONG WITH ME ON INSTAGRAM, PINTEREST, FACEBOOK, YOUTUBE AND  TWITTER FOR MORE RECIPE INSPIRATION AND A GLIMPSE INTO OUR EVERYDAY LIFE!

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5 from 3 votes

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! 
Course Main Course, Side Dish
Cuisine American
Keyword Greek Yogurt Mac and Cheese, healthy mac and cheese, homemade mac and cheese recipe, stovetop mac and cheese
Prep Time 10 minutes
Cook Time 20 minutes
Total Time 30 minutes
Servings 10 Servings
Calories 367kcal
Author Laura

Ingredients

Macaroni and Cheese:

  • 8 oz Eat Banza Elbow Macaroni (or other gluten-free pasta)
  • 2 TBSΒ  tapioca flour
  • Β½ tspΒ  onion powder
  • ΒΌ tspΒ  garlic powder
  • ΒΎ tspΒ  sea salt
  • ΒΌ tsp freshly ground black pepper
  • 2 TBS butter
  • 1 cup 2% milk
  • 1 cup plain Greek yogurt
  • 2 cups shredded cheddar cheese

Topping:

  • 2 TBS grated Parmesan cheeseΒ 
  • Β½ cup shredded cheddar cheese
  • ΒΌ cupΒ  almond meal/flour
  • ΒΌ -Β½ tsp garlic salt
  • ΒΌ tsp freshly ground black pepper
US Customary - Metric

Instructions

  • Preheat oven to 375 degrees F. Grease an 8x8” 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!

Nutrition

Calories: 367kcal | Carbohydrates: 43.8g | Protein: 15g | Fat: 16g | Cholesterol: 3mg | Potassium: 21mg | Fiber: 4.6g | Sugar: 4.2g | Calcium: 90mg | Iron: 2.7mg

This post contains affiliate links, which means that if you purchase a product through a link you clicked on here, I receive a portion of the sale. Thank you for supporting JoyFoodSunshine! 

You might also like:

Paleo Cookie Dough Ice Cream
Vegan Chocolate Fondue
Peppermint Brownies

Filed Under: Gluten-Free, Lunch, Main Dish, Recipes, Side Dish Tagged With: gluten free, homemade holidays, main dish, side dish

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Reader Interactions

Comments

  1. Victoria

    May 25, 2020 at 11:27 am

    If I leave off the topping, does the rest of the dish still need to be baked?

    Reply
    • Laura

      May 25, 2020 at 2:52 pm

      Technically no!

      Reply
  2. Robin

    March 22, 2020 at 4:19 pm

    5 stars
    We’ve made this twice over the past few months and love it- thank you! We use a cast-iron oven-proof pot and boil the noodles, make the sauce (while noodles are draining in a colander), and bake the final dish all in one pan, minimizing dish clean-up!

    Reply
  3. Lauren Parker

    December 10, 2019 at 10:25 pm

    Have you tried the Sprouts Quinoa Fusili in the stovetop mac and cheese recipe? Will tapioca flour work instead of regular flour to make the Rue?

    Reply
    • Laura

      December 11, 2019 at 6:40 am

      Yes to both of those questions! I also use Eat Banza chickpea pasta for the stovetop mac and cheese recipe with great results!

      Reply
  4. Hope

    September 18, 2017 at 8:25 pm

    Is there a freezer option for this? Trying to get some freezer options for before baby #2 comes in November! Or can you direct me to some of your recipes that freeze well? Love your site and also that you know the busyness that is motherhood.

    Reply
  5. Richard Price

    August 11, 2017 at 4:27 am

    5 stars
    I agree about the crispy top layer – there’s just no substitute for that! Great recipe!

    Reply
  6. Kristina @ Love & Zest

    July 28, 2017 at 10:49 am

    5 stars
    I am in love with this Macaroni and Cheese! I need to make it very soon! I love that you used Greek yogurt in the recipe!

    Reply
  7. Jenny Shea Rawn

    July 27, 2017 at 9:45 am

    Cannot wait for cooler weather to try this! Pinning. My two year old is becoming very picky, so need some new recipes to try out – he’s started pulling out any fresh herb pieces from his dinner, calling them “buuugs” πŸ™‚

    Reply
    • Laura

      July 27, 2017 at 4:30 pm

      LOL Yessss! those bugs can be no fun! πŸ˜‰

      Reply
  8. Emily

    July 27, 2017 at 9:16 am

    Honestly I don’t think I’ve ever made mac and cheese at home before! But this recipe is right up my alley, I use Greek yogurt for everything and have gluten free pasta on hand! Yay!

    Reply
    • Laura

      July 27, 2017 at 4:29 pm

      You will love it Emily!

      Reply
  9. Emily

    July 27, 2017 at 8:30 am

    That is so wonderful that you get to partner with Sprouts; we love getting specialty products from there that we can’t get anywhere else. We also always get our fruits and veggies there (unless we get them at Safeway or the Farmer’s market). I love mac n’ cheese, and it seems like the baked mac n’ cheese is my family’s favorite. It’s such a creamy comforting dish.

    Reply
  10. Deanna Segrave-Daly

    July 26, 2017 at 12:26 pm

    I just adore your comment about your husband’s tastebuds – I call my hubs a “tricky eater.” We also eat A LOT of homemade mac n cheese too – I’ve been mixing regular pasta with some gluten-free versions – this recipe looks delish!!

    Reply
    • Laura

      July 26, 2017 at 9:02 pm

      LOL Deanna! Thankfully he’s not really picky, he just prefers “younger people” food! πŸ˜‰

      Reply
  11. Marisa

    July 26, 2017 at 11:36 am

    Pinned. I cannot wait to make this. Looks so good. I’d add a side of roasted vegetables and call dinner done!

    Reply
    • Laura

      July 26, 2017 at 9:03 pm

      You will love it Marisa! I’m totally not joking when I say we eat this weekly! I usually make a huge salad to go with it! πŸ˜‰

      Reply

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About Laura

 

Hello I’m Laura! I am a former chemistry teacher turned wife and mom of five beautiful babies with one on the way in 2021! I’m a green smoothie addict, lover of the outdoors, and a peanut butter & nap enthusiast! Click here to read more >>

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