This Homemade Greek Yogurt Gluten-Free Mac And Cheese Recipe is packed with protein and has a pizza twist!

Alright, let me get this out of the way first—this recipe is chaos in the best possible way. It combines two ultimate comfort foods (pizza and mac and cheese) into one bowl of high-protein, gluten-free, creamy deliciousness, and somehow it all just works. The mozzarella, Parmesan, roasted tomatoes, and turkey pepperoni come together with that gooey, cheesy texture you want from mac and cheese, but the flavor is full-on pizza night. You’re going to love it. Your kids are going to love it. Anyone you serve it to is going to love it.
I’ve made this more times than I can count, mostly because it just hits when I need something fast, warm, and completely satisfying. The roasted tomatoes add depth that jarred sauce just can’t, and the yogurt is the sleeper hit. It gives the sauce a creamy finish without making it heavy, and it adds a little protein boost while it’s at it. Just stir it in at the end, and you’re golden.
If I’m being honest, the pepperoni is probably my favorite part. You roast it until the edges get a little crispy, and it adds that salty, chewy bite that pulls everything together. This dish is one of those weird hybrids that sounds slightly unhinged on paper, but once you taste it, you’re already planning your next batch.

Is Homemade Greek Yogurt Gluten-Free Mac And Cheese Recipe Healthy?
This recipe has some healthy swaps that make it healthier than your standard mac and cheese. The Greek yogurt adds protein and calcium without the need for heavy cream, and turkey pepperoni is lower in fat than traditional pepperoni. There’s olive oil instead of butter, which means less saturated fat, and the tomatoes contain potassium, vitamin C, and lycopene.
That said, you still have noodles and plenty of cheese, so I’d still recommend enjoying this dish in moderation. If you can help it.

Getting The Pizza Flavor Without Sauce
You may have noticed that this recipe skips pizza sauce completely, and that’s intentional. I have found that by roasting the tomatoes with a little oil, Italian seasoning, and garlic salt, you get a richer, more concentrated flavor that outshines pizza sauce. It also helps you avoid all the added sugar, salt, and preservatives you find in the jarred stuff. So, skip the sauce on this one. Fresh is best!

How Do I Store Leftovers?
Let everything cool completely, then transfer it to an airtight container and refrigerate. It’ll stay good for up to 4 days. You can also freeze it in individual portions by wrapping it tightly or using freezer-safe containers. Thaw overnight in the fridge, then reheat gently on the stovetop.
Serving Suggestions
This dish is certainly hearty and filling enough to have all by itself, but sometimes, you want to dress it up a bit! Got room on your plate for some side dishes? I like having this mac and cheese with a side of Roasted Green Beans or Sautéed Broccolini. And for true pizzeria vibes, you could whip up a batch of Garlic Toast or an Antipasto Salad.

Ingredients
- 4 Roma tomatoes sliced
- 1/2 cup turkey pepperoni about 30 slices
- 2 teaspoons olive oil
- 2 teaspoons Italian seasoning, divided
- 1 1/2 teaspoons garlic salt divided
- pepper
- 8 ounces gluten-free macaroni noodles
- 6 ounces mozzarella cheese grated, about 2 cups
- 2 ounces Parmesan cheese grated, about 2/3 cups
- 1/2 cup 2% plain Greek yogurt
Instructions
- Preheat your oven to 400°F.
- In a medium bowl, toss together the sliced tomato, turkey pepperoni, olive oil, 1 teaspoon of Italian seasoning, and 1/2 teaspoon of garlic salt. Spread in one layer on a baking sheet and sprinkle with a pinch of pepper.
- Bake until the tomatoes begin to soften, about 13-15 minutes. Note that the pepperoni will only take 6-7 minutes to crisp up, so check them often and remove from the pan when done, continuing to cook the tomatoes until soft. Set aside.
- Bring a large pot of salted water to a boil, and cook the pasta according the package directions. Drain the cooked pasta and reserve 1/2 cup of the cooking water.
- Transfer the cooked pasta back into the pot and stir in 1/3 cup of the pasta water. Then add in the cheese, a little bit at a time. Stir between each addition until the cheese is fully melted, and then continue to add the cheese.
- Once the cheese is melted, stir in the Greek yogurt until creamy and well mixed. Stir in the remaining 1 teaspoon of garlic salt and Italian seasoning, and season with a pinch of pepper. If it’s too thick, add the remaining pasta water.
- Stir in the cooked tomatoes and pepperoni and enjoy.
Nutrition Info:
Nutrition information are estimates only and may vary based on the specific brands, ingredients, and portion sizes you use. This data is provided for informational purposes only.


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