Butternut Squash Macaroni and Cheese

4.65 from 73 votes
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This butternut squash macaroni and cheese is a delightful twist on a classic comfort food. The recipe seamlessly blends the sweetness of butternut squash with the creamy, cheesy goodness of mac and cheese.

Butternut squash macaroni and cheese in a white bowl.

This dish offers a comforting blend of flavors, ideal for cold nights when you’re in the mood for something cozy yet refined. It presents a chance to create a wholesome meal featuring butternut squash, a favorite ingredient of the season.

Instead of the usual macaroni and cheese base of flour, butter, milk, and cheddar, this version incorporates pureed starchy butternut squash, sweet caramelized onions, and milk, blended until silky smooth. Just a tiny addition of sharp cheddar cheese ensures the beloved gooey consistency.

“Having grown up with the boxed stuff, I was afraid that my teenage boys would not like it. I was wrong!! They loved it, and the winner for me is that it’s so much healthier and packed with vitamins. This one’s a keeper!”—Maxine

Recipe ingredients

  • Pasta: Use elbow macaroni for a classic look. Select gluten-free if you have dietary restrictions or whole-grain pasta for more fiber per serving.
  • Butternut Squash: Purchase one about 2 pounds in size to yield 4 cups of diced pieces. Frozen butternut squash can also be used.
  • Onions: Use thinly sliced yellow onions to caramelize. They have a good balance of savory and naturally sweet flavors.
  • Butter: Cook the onions in butter to promote browning, but feel free to use olive oil.
  • Broth: Use vegetable broth or stock to cook the butternut squash. The savory liquid infuses more flavor into the vegetable.
  • Milk: Whole milk adds creaminess to the pasta sauce without making it too rich.
  • Cheese: Shredded sharp cheddar cheese adds the right amount of tangy and salt flavor. Freshly grated cheese will have the best melt.
  • Herbs: Garnish with freshly chopped parsley.

See the recipe card below for all ingredients and measurements (US and metric).

Healthy version of macaroni and cheese.

Caramelize the onions

Step 1: This dish begins with slowly sauteing onions in a little bit of butter. Caramelized onions add a pleasant depth to this butternut squash macaroni and cheese recipe. The process takes about 30 minutes. While your onions are happily transforming in the pan, make the sauce.

Cook the butternut squash

Step 2: Boil cubes of butternut squash until fork-tender in vegetable broth for the base of the cream sauce. The natural starches in the squash activate when heated. It takes about 7 minutes to cook.

Puree the squash

Step 3: My blender is a pro at making purees, but you can also use a food processor if it’s big enough. Add the cooked squash, caramelized onions, milk, salt, and vegetable broth. The rapid mechanical shear from the blades, in addition to the liquids, helps to create a silky squash puree.

Cook the pasta

Step 4: When cooking pasta, I like to season the boiling water, a habit I picked up in culinary school. I use a ratio of 1 tablespoon of kosher salt for every 4 quarts of water. Cook the pasta according to the packaged directions until al dente. Drain off the water, but keep the pasta in the pot.

Make the macaroni and cheese

Step 5: The beauty of this dish is that you can add whatever cheese you like. I kept it simple with a sharp cheddar cheese so the squash and sweet onions shine through. Add the squash puree and shredded cheddar to the pot of pasta. Stir until coated—season with salt and pepper to your liking.

If you are a fan of the traditional dish, I won’t say that it’s like having a 1:1 replacement. The cheese sauce is a little grainy because of the squash. However, for a healthy alternative, this is an excellent option.

Add a breadcrumb topping

Step 6: For a little crunch, I toast Panko bread crumbs over medium heat until golden brown. It adds the perfect texture contrast, but it is optional. Alternatively, you can use crackers like Ritz or Chez-Its; just crumble them up and use them as a quick topping.

Butternut squash macaroni and cheese in a white bowl with panko breadcrumbs.


Step 7: Generously sprinkle the toasted breadcrumbs on top before serving the butternut mac and cheese. I also add chopped parsley for a pop of color.

Flavor variations

  • Pasta: Use other short-cut types of pasta like shells, cavatappi, fusilli, or penne. Add fiber with whole-grain or fiber-enriched pasta.
  • Cheese: Pair the cheddar cheese with a mild Monterey Jack or white cheddar for a gooey melt. For sharp savory flavor, add aged Parmesan or Pecorino Romano, or add smoked gouda for a charred taste.
  • Topping: Add homemade breadcrumbs, crushed Ritz crackers, or Chez-it’s.
  • Seasoning: Make the dish spicy with cajun seasoning or taco seasoning. Drizzle in truffle oil. Add in onion powder and garlic powder for a roasted allium note.
  • Herbs: Add fresh herbs like chives, parsley, thyme, rosemary, or basil.
  • Seafood: Add canned tuna to make it a tuna mac, or add seafood to make lobster mac and cheese.
  • Vegetables: Add steamed broccoli, peas, mushrooms, spinach, kale, or cauliflower.
  • Meat: Add shredded chicken, leftover baked ham, turkey, pancetta, or crispy bacon.

Serving suggestions

Frequently asked questions

Can I bake the butternut squash pasta?

Add the butternut squash pasta into a baking dish or cast iron skillet to make a baked macaroni and cheese. If desired, add more cheddar cheese for a gooey melt. Toss ½ cup panko with 2 tablespoons of melted butter and sprinkle on top. Bake at 350ºF (177ºC) until golden brown, about 15 minutes.

How is adding butternut squash healthier in a pasta sauce?

Cutting butternut squash to incorporate into a pasta dish has impressive health benefits! It’s low in fat and packed with dietary fiber, potassium, vitamin B6, folate, vitamin C, and carotenoids in the orange flesh, like beta-carotene that converts to vitamin A. You can closely replicate the creamy texture without extra flour and butter.

Can you freeze butternut squash macaroni and cheese?

Freeze a tray or individual portions for up to 3 months. Smaller servings can be reheated in the microwave. A baking dish can be warmed in the oven at 350ºF (177ºC) until hot. Cover the surface if it starts to brown too much.

A spoonful of golden noodles combined with butternut squash.

Recipe Science

Using butternut squash to make a creamy sauce

Butternut squash is considered a naturally starchy gourd. When cooked and pureed, the starch molecules absorb the liquid from the milk and broth. Then, it swells and holds the moisture in suspension without separating. You get a creamy, smooth sauce without making a roux base (cooked flour and butter plus milk).

Butternut Squash Macaroni and Cheese

I love making butternut squash macaroni and cheese because it adds a subtle sweetness and creaminess to the dish, creating a comforting and satisfying meal that's a tasty twist on a classic favorite.
4.65 from 73 votes
Prep Time15 minutes
Cook Time30 minutes
Total Time45 minutes
Servings 4 servings
Course Entree
Cuisine American


  • 2 cups elbow macaroni
  • 1 tablespoon unsalted butter
  • 1 ½ cups sliced yellow onion, ⅛" thick
  • 4 cups diced butternut squash, ½" dice
  • 5 cups vegetable broth , or stock
  • ¾ cup milk
  • 1 teaspoon kosher salt
  • 1 cup shredded sharp cheddar cheese
  • ¼ cup panko breadcrumbs
  • 1 tablespoon chopped parsley


  • Caramelize the Onions – In a large skillet, melt the butter over medium heat. Add the onions in one layer. Reduce heat to medium-low and cook until caramelized, about 25 to 30 minutes. Stir occasionally, keeping the onions in one layer. Reduce heat if browning too quickly.
  • Cook the Butternut Squash – In a large pot, bring the vegetable stock to a boil. Add the butternut squash and cook until tender, about 7 minutes. Transfer to a blender and reserve the broth.
  • Puree the Squash – To the blender with squash, add the caramelized onions, milk, salt, and ¼ cup reserved broth. Puree until smooth and creamy. If needed, add up to ¼ cup more broth to thin the sauce.
  • Cook the Pasta – In a large pot, cook the macaroni in salted boiling water according to the manufacturer's instructions. Drain and leave the pasta in the pot.
  • Make the Macaroni and Cheese – Pour the butternut squash puree over the cooked noodles in the pot. Add the cheddar cheese, and stir until melted and combined. Add more milk if needed to adjust the consistency. Season with salt and pepper to taste.
  • Toast the Breadcrumbs – In a small pan, toast panko breadcrumbs over medium heat until all sides are golden brown, about 3 minutes. Shake the pan occasionally for even toasting.
  • To Serve – Serve topped with toasted breadcrumbs and parsley.


  • Recipe Yield: About 4 cups
  • Serving Size: 1 cup
  • Storing: Store in an airtight container in a refrigerator for up to 5 days. Freeze for up to 3 months.
  • Make it Gluten-Free: Use gluten-free macaroni and breadcrumbs.

Nutrition Facts

Serves: 4 servings
Calories 432kcal (22%)Carbohydrates 55g (18%)Protein 19g (38%)Fat 15g (23%)Saturated Fat 9g (45%)Polyunsaturated Fat 1gMonounsaturated Fat 3gCholesterol 43mg (14%)Sodium 827mg (34%)Potassium 274mg (8%)Fiber 3g (12%)Sugar 7g (8%)Vitamin A 650IU (13%)Vitamin C 5mg (6%)Calcium 360mg (36%)Iron 2.5mg (14%)

Percent Daily Values are based on a 2000-calorie diet. All nutritional information is based on estimated third-party calculations. Each recipe and nutritional value will vary depending on the brands you use, measuring methods, and portion sizes per household.

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Jessica Gavin

I'm a culinary school graduate, cookbook author, and a mom who loves croissants! My passion is creating recipes and sharing the science behind cooking to help you gain confidence in the kitchen.

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