Baked greek yogurt mac and cheese is an easy, nutritious version of a classic comfort food! It’s a protein-packed side dish to feed a crowd – and easily made gluten-free.

I’m a firm believer that making homemade versions of your favorite pre-packaged foods is always a better choice! And this greek yogurt mac and cheese is a delicious, homemade version of everyone’s favorite boxed dish!

This recipe is creamy and cheese and loaded with protein! It’s easily made gluten-free by using gluten-free noodles and flour!

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)!

Greek Yogurt Mac and Cheese: Substitutions 

• Elbow Macaroni: any pasta variety works well in this recipe, including gluten-free pasta. I like shapes like elbows, shells or wheels,.
• Flour. for a gluten-free version, use an all-purpose gluten free flour.
• Whole milk. 2% milk or half and half are great substitutions.
• 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!

How to Make Greek Yogurt Mac and Cheese

Let’s walk through how to make greek yogurt mac and cheese.

Begin by cooking the macaroni in boiling water until al dente – drain and do not rinse.

Make the Cheese Sauce

Next, make the cheese sauce.

Melt the butter in a medium saucepan over medium heat.

Once butter is melted, add the dry ingredients and whisk until combined.

Cook on medium heat for 1 minute, or until it forms a paste-like consistency and becomes light brown.

Add milk and greek yogurt and whisk until ingredients are 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. Whisk until the cheese is melted.

Assemble

Add cheese sauce to the cooked and drained pasta and stir to combine.

Make on the Stovetop (no Baking)

You do not have to bake this recipe. You can stop at this step and serve it straight from the stovetop without the topping.

In a small bowl, combine topping ingredients.

Pour the macaroni & cheese mixture into prepared baking dish.

Sprinkle topping over pasta.

Bake

Bake in preheated oven for 15-20 minutes or until the cheese on the top is melted and slightly browned.

To Prepare in Advance

This greek yogurt macaroni and 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, cover it with foil for the first 10 minutes of baking.

Serve

Serve this greek yogurt mac and cheese with roasted broccoli. or a delicious salad. You can also serve this homemade mac and cheese as an easy side dish for a BBQ or potluck!

Store/Freeze

Store leftovers in an airtight container for up to 5 days in the refrigerator, or up to 2 months in the freezer.

Reheat in the microwave, on the stovetop, or covered in the oven stet to warm.

Greek Yogurt Mac & Cheese FAQs

If you make and love our recipes, it would mean so much to me if you would leave a comment and rating! And don’t forget to follow along with us on Instagram, Pinterest, Facebook, and Youtube – be sure to tag @joyfoodsunshine and use the hashtag #joyfoodsunshine so we can see your creations!

Try these recipes

Easy Homemade Mac and Cheese

Vegetable Mac and Cheese

Baked Mac and Cheese

Butternut Squash Mac and Cheese

Spaghetti Squash Mac and Cheese

Oven Roasted Broccoli