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Satisfy your cheesy pasta cravings, but make it high-protein and packed with veggies with this creamy and healthy Butternut Squash Mac and Cheese. It tastes just like regular mac and cheese, but with 29 grams of protein and 8 grams of fiber!

Butternut squash mac and cheese in a bowl.
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Quick Summary: Butternut Squash Mac and Cheese

  • Why Make This Recipe: This creamy squash mac and cheese is made with hidden veggies and extra protein, but still tastes like your favorite comfort food, just healthier.
  • Nutrition: 449 calories, 29 grams of protein, 8 grams of fiber
  • Diet: High Protein, High Fiber, Vegetarian
  • Time: 50 Minutes (15 minutes of prep time + 35 minutes of cook time)
  • Method: Stovetop and Oven
  • Best for: fall family dinners, meal prep lunches, or a lighter Thanksgiving side.
  • Tip: Never bring your cheese sauce above a gentle simmer, or the cream cheese and melted cheese will turn grainy. 

This high-protein butternut squash mac and cheese skips the heavy cream and butter to make a healthy alternative to the beloved side dish. It’s loaded with protein from the protein pasta and cottage cheese, and the butternut squash sneaks in fiber without stealing the show from all that cheese.

The protein and fiber help keep you full and fuel your body while your taste buds enjoy the classic mac and cheese flavor. If you like high-protein macaroni recipes, you will love my healthy chili mac and cottage cheese ziti!

Why You’ll Love This Recipe

  • No Butter, Flour, or Cream: The butternut squash cheese sauce is thick and creamy from the squash and cottage cheese, so you don’t need extra fat from butter, a flour roux, or heavy cream. 
  • Hidden Veggies: Butternut squash has a mild, slightly sweet flavor that practically disappears behind the bold flavors of cheddar cheese, gouda, and parmesan. I also hide veggies in these chocolate chip zucchini muffins.
  • Tastes Like the Real Thing: Don’t let the addition of veggies and cottage cheese fool you; this recipe tastes just as delicious and indulgent as regular mac and cheese. 

Ingredients

Ingredients to make this butternut mac and cheese in bowls on a table.
  • Butternut Squash: This winter squash has a sweet, nutty flavor that is incredibly mild. When it’s blended, it has a creamy consistency that’s perfect for a cheese sauce. 
  • Cottage Cheese: Blended cottage cheese doesn’t have a strong flavor, but it adds a lot of protein and makes the cheese sauce extra creamy. I also add cottage cheese to this healthy Alfredo sauce to add protein and make it creamier.
  • Protein Pasta: Using protein pasta is an easy way to boost the protein content in your favorite pasta dishes.
  • Low-Fat Milk: Use low-fat milk or unsweetened plant-based milk to reduce the fat content while keeping the sauce rich and creamy. 
  • Cheese: This butternut squash mac and cheese recipe uses a blend of three cheeses, cheddar, gouda, and Parmesan, to create a unique and bold flavor.
  • Panko Crumbs: Broiling breadcrumbs over your mac and cheese gives it a little crunch and a lovely golden crust on top.

See the recipe card below for exact ingredient amounts, nutritional information, and detailed instructions.

Variations & Dietary Modifications

  • Add More Protein: Stir in shredded chicken cooked in the Instant Pot or ground turkey before broiling your mac and cheese to give it an extra protein boost and make it a full meal on its own.
  • Use Different Veggies: Try using pumpkin puree instead of butternut squash, or stir in some spinach or kale to pack in even more veggies. 
  • Swap the Cheese: You can use any cheeses you like for mac and cheese. Use a sharp cheddar, like in my healthy mac and cheese with cottage cheese, for more tang. You can also try Gruyère or smoked gouda for a richer, savory flavor.
  • Make It Gluten-Free: Use gluten-free protein pasta, like chickpea pasta, and skip the Panko crumbs on top to make this a gluten-free mac and cheese. 

How to Make Butternut Squash Mac and Cheese

This baked butternut squash mac and cheese is the perfect way to hide some veggies in your favorite comfort food! It comes together quickly, so before you start cooking, lightly spray a 9”x13” baking dish with nonstick spray. You’ll also want to preheat your broiler about 5 minutes before placing your mac and cheese under it.

Butternut squash cooking in a pot.
  1. Step 1: Cook the Butternut Squash. Bring a cup of water to a boil in a medium pot. Once it’s boiling, reduce the heat to medium and add the butternut squash. Simmer the squash for 5-10 minutes or until it easily mashes against the side of the pot with a fork. Turn off the heat, strain the squash, and let it cool for 5 minutes.
The butternut squash added in a blender.
  1. Step 2: Blend the Squash. Transfer the cooled squash to a vented blender along with ¼ cup of vegetable broth. Blend until completely smooth, then transfer to a bowl and set aside.
Cottage cheese added to the blender with the butternut squash.
  1. Step 3: Blend the Cottage Cheese. Add the cottage cheese to the blender and blend it until the cottage cheese is completely smooth. Cook the pasta according to the package while blending the squash and cottage cheese. Set aside ½ cup of pasta water before straining the pasta. 
Cooking the onion and garlic in a pan.
  1. Step 4: Sauté the Aromatics. Heat a large pan over medium heat with the olive oil, onion, and garlic. Cook them for 3-4 minutes, or until they soften and become fragrant.
Cheeses added to the sauce.
  1. Step 5: Add the Milk and Cheeses. Add the milk and blended cottage cheese to the pot. Sprinkle in the cheddar cheese, gouda, and Parmesan. Stir until combined and melted.
Butternut squash and seasonings added to the mac and cheese sauce.
  1. Step 6: Stir In the Squash. Add the blended butternut squash, thyme, paprika, cayenne pepper, salt, and pepper. Stir until it’s well combined, and simmer for 10 minutes.

 

Pasta mixed into the sauce and all the ingredients added to a casserole dish.
  1. Step 7: Add the Pasta. Stir in the cooked pasta and the pasta water, making sure the pasta is fully coated in the cheese sauce. Turn off the heat and transfer the cheesy pasta to the prepped 9”x13” baking dish. Top with Panko bread crumbs and extra cheese.
The mac and cheese cooked with panko on top.
  1. Step 8: Broil. Place the mac and cheese under the broiler for about 4 minutes, or until the top turns golden brown and the breadcrumbs are toasted. Promptly remove from the oven to avoid burning the top. Serve with this zucchini pasta salad. There isn’t actually any pasta in the salad, just zucchini noodles!

Expert Tips

  • Gentle Simmer Only: Avoid boiling your cheese sauce. Never let the temperature go beyond a gentle simmer, or the cheese could curdle and turn grainy. 
  • Multitasking Saves Time: Prepare various parts of the recipe at the same time so the cooking process is quicker. You can cook the pasta in a separate pot while the squash simmers, and preheat the oven while the cheese sauce cooks to save yourself some time.
  • Adjust Seasonings Before Broiling: Taste test your cheesy pasta before transferring it to the baking dish and broiling it. It’s easier to add more seasonings while the pasta is hot in the pot than after it’s baked with a toasty crust.
  • Storing: Place leftovers in an airtight container in the refrigerator for up to 5 days. You cannot freeze this mac and cheese because it ruins the texture and makes the cheese grainy and the pasta too soft.
  • Reheating: Reheat your butternut macaroni and cheese in the oven at 350°F until it’s heated through. Or place individual servings in the microwave in 30-second intervals. You may need to add a splash of milk or broth to keep it creamy.
A casserole dish filled with mac and cheese with butternut squash and a spoon resting in the dish.

Serving Suggestions

Who doesn’t love mac and cheese? This healthy butternut squash mac and cheese is sure to be a hit for dinnertime with the whole family, especially if you need a sneaky way to get the kids to eat their veggies. It pairs well with any BBQ or comfort dish for dinner and can be enjoyed on its own with a salad for lunch. 

Butternut Squash Mac and Cheese Recipe FAQs

Can you taste the butternut squash in butternut squash macaroni and cheese?

No, not really. You can barely taste the butternut squash in this mac and cheese. It’s masked by the bold cheeses and savory flavors. 

Can I use frozen or canned butternut squash to make butternut mac and cheese?

You can absolutely use frozen or canned butternut squash puree. You don’t need to thaw frozen butternut squash chunks before cooking them, and there’s no cooking needed if you use a canned puree. 

Can I make this butternut squash mac and cheese on the stove only?

Sure, you can make this mac and cheese a stove-only recipe by skipping the bread crumbs and broiling at the end. It takes out the crunchy texture, but it will save you some dishes. 

Can I make this butternut squash mac and cheese ahead of time?

Sure, if you want to save yourself a little time, you can prepare the butternut squash and cottage cheese in advance. Store both of them in separate airtight containers in the refrigerator for up to 2 days.

A bowl filled with mac and cheese with butternut squash inside.

More Delicious Butternut Squash Recipes

If you tried this Butternut Squash Mac and Cheese recipe or any other recipe on my website, please leave a 🌟 star rating and let me know how you go in the 📝 comments below.

A bowl filled with butternut squash mac and cheese.
5 from 1 vote
Servings: 6

Butternut Squash Mac and Cheese

Make a bowl of warm, creamy butternut squash mac and cheese packed with protein and fiber in less than an hour.
Prep: 15 minutes
Cook: 35 minutes
Total: 50 minutes
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Ingredients 

  • 2 cups Butternut Squash, cut into ½-inch cubes (fresh or frozen)
  • ¼ cup Low Sodium Vegetable Broth
  • 1 cup Non-Fat Cottage Cheese
  • 16 oz Protein Rigatoni Pasta, gluten-free if needed
  • 1 tsp Olive Oil
  • ½ cup Yellow Onion, diced
  • 2 tbsp Garlic, minced
  • 1 cup Low Fat Milk or milk of choice
  • 1 cup Low Fat Cheddar Cheese + more for topping
  • ⅓ cup Gouda Cheese
  • ¼ cup Parmesan Cheese + more for topping
  • ½ tsp Dried Thyme
  • ½ tsp Paprika
  • ¼ tsp Cayenne Pepper
  • ½ cup Pasta Water
  • ½ tsp Salt
  • ½ tsp Pepper
  • ½ cup Panko Breadcrumbs, gluten-free if needed

Instructions 

  • In a medium pot, bring 1 cup water to a boil. Once boiling, reduce to medium heat and add the butternut squash. Simmer 5-10 mins or until fork tender – how long will depend on if its fresh or frozen then thawed.
  • Turn off the heat then strain squash. Cool for 5 minutes then add to a blender with ¼ of broth and blend until smooth. Remove from the blender, transfer to a bowl and set aside.
  • Add cottage cheese to the blender and blend until smooth. Set aside
  • Cook the pasta according to the package. Reserve 1/2 cup of pasta water before straining the pasta and set aside.
  • Heat a large pan over medium heat, add the oil, onion and garlic and cook for 3-4 mins just until sautéed. Then add the milk, blended cottage cheese, cheddar cheese, gouda cheese and parmesan cheese. Stir until combined.
  • Add the blended butternut squash, thyme, paprika, cayenne pepper, salt and pepper. Simmer for 10 minutes.
  • Next add the cooked pasta and pasta water and mix to the large pan. Stir well to combine. Turn off the heat.
  • Transfer the mixture from the large pan to a 9-inch x 13-inch baking dish that’s lightly sprayed with cooking spray. Top with breadcrumbs and extra cheese. Broil for 4 mins until the top is golden brown then serve!

Notes

  • Do not boil the mac and cheese or bring the heat above a gentle simmer, or the cheese will curdle and turn grainy.
  • Multitask your steps to save time. Cook the pasta in a separate pot while the squash cooks, and preheat the oven while the cheese sauce simmers to save yourself some time.
  • Taste-test your mac and cheese before transferring it to the baking dish and broiling it. Then you can add more seasonings as needed.

Nutrition

Calories: 449kcal, Carbohydrates: 59g, Protein: 35g, Fat: 12g, Saturated Fat: 4g, Polyunsaturated Fat: 0.4g, Monounsaturated Fat: 2g, Cholesterol: 26mg, Sodium: 768mg, Potassium: 357mg, Fiber: 12g, Sugar: 12g, Vitamin A: 5307IU, Vitamin C: 12mg, Calcium: 397mg, Iron: 8mg

Nutrition information is automatically calculated, so should only be used as an approximation.

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Megan

Megan is a nutritionist who coaches women 35+ lose weight sustainably. She is the author of the Low Calorie Cookbook, fitness instructor, host of the Dish On Ditching Diets Podcast and creator of Skinny Fitalicious where you get lighter, higher protein recipes. Follow Megan on Facebook, Pinterest, YouTube and Instagram for the latest updates.

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5 from 1 vote

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  1. Megan says:

    This cottage cheese mac and cheese with butternut squash recipe is a spin on my high protein mac and cheese. The butternut squash adds a creamy and delicious texture featuring fall flavors. I hope you enjoy it!