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Butternut Squash Mac and Cheese

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A bowl of creamy butternut squash mac and cheese
This butternut squash mac and cheese is creamy, cozy, and secretly high in protein thanks to blended cottage cheese. Roasted butternut squash and garlic get blended into a velvety, veggie-packed sauce, then melted with sharp cheddar and Gruyere for the ultimate better-for-you comfort food the whole family loves.

Why You’ll Love This Butternut Squash Mac and Cheese

Bowls of butternut squash mac and cheese
  • Ultra creamy. Blended roasted squash and cottage cheese make the silkiest sauce, no roux required.
  • Secretly high in protein. Cottage cheese plus real cheddar and Gruyere pack in protein.
  • Sneaks in veggies. A whole butternut squash blends right into the sauce, so kids never know.
  • Better-for-you comfort food. All the cozy mac and cheese flavor with less guilt.
  • Make-ahead friendly. The blended sauce keeps for days and freezes beautifully.

Classic mac and cheese will always have my heart, but this version lets you enjoy that same creamy, cheesy comfort while getting in some extra vegetables and protein. Roasting the squash and garlic first gives the sauce a deep, sweet, savory flavor you just cannot fake.

What You Need to Make Butternut Squash Mac and Cheese

Roasted butternut squash halves and roasted garlic on a sheet pan

Here is everything you need, plus a few of my favorite products. Full measurements are in the recipe card above.

  • Butternut squash. One small squash (about 2 lb), roasted until sweet and tender for the sauce base.
  • Garlic. A whole head, roasted until soft, sweet, and jammy.
  • Olive oil, salt, pepper, smoked paprika, and nutmeg. To season and roast the squash.
  • Cottage cheese. The secret to a creamy, high protein sauce that blends completely smooth.
  • Whole milk and pasta water. To thin the sauce to a silky, pourable consistency.
  • Dijon mustard and lemon. A little tang to balance the sweet squash and cut the richness.
  • Sharp cheddar and Gruyere. For that classic melty, cheesy flavor (or use Parmesan).
  • Short pasta. Shells, cavatappi, or elbows all catch the creamy sauce beautifully.

How to Make Butternut Squash Mac and Cheese

Seasoned butternut squash halves with smoked paprika before roasting

Here is the quick walk-through, and the full recipe is in the card above.

  1. Roast. Roast the seasoned squash cut side down with a foil-wrapped head of garlic at 400 degrees F until fork-tender.
  2. Cook the pasta. Boil the pasta until just shy of al dente, saving a cup of pasta water before draining.
  3. Blend the sauce. Blend the squash, squeezed roasted garlic, cottage cheese, milk, pasta water, Dijon, lemon, and salt until completely smooth.
  4. Melt in the cheese. Warm the sauce over low heat and stir in the cheddar and Gruyere a handful at a time.
  5. Combine and serve. Toss with the pasta, loosening with pasta water until glossy and creamy, and serve right away.
Cooked short pasta in a pot
Creamy blended butternut squash cheese sauce being poured
Shredded cheddar and Gruyere added to the butternut squash sauce

Why Cottage Cheese Makes It High Protein

The secret ingredient here is cottage cheese, and it does so much for this dish. Blended until completely smooth, it disappears into the sauce and adds a rich, creamy tang, almost like a bechamel, but with a fraction of the effort and a big boost of protein. There is no need to make a butter-and-flour roux, and you get a lighter sauce that still tastes decadent. Between the cottage cheese and the real cheddar and Gruyere, this mac and cheese has noticeably more protein than the classic version, which makes it more filling and satisfying. Just be sure to blend it well and keep the heat low when melting in the cheese so it stays silky, not grainy.

Tips for the Silkiest Sauce

A bowl of freshly shredded cheddar and Gruyere cheese
  • Blend longer than you think. A full 60 seconds is what makes the sauce silky instead of chalky.
  • Taste before the pasta. The sauce should taste slightly over-seasoned on its own, since the pasta mutes it.
  • Shred your own cheese. Pre-shredded has anti-caking starch that makes the sauce gritty.
  • Keep the heat low. Melt the cheese gently so the cottage cheese does not turn grainy.
  • If it tastes too sweet, add more Dijon, lemon, or Parmesan rather than more salt.

Stovetop or Baked

This mac and cheese is creamy and delicious served straight from the pot, which is how I make it most often on a weeknight. But if you love a golden, crispy top, it bakes up beautifully too. Just stir in an extra splash of milk before baking, since the sauce thickens in the oven, then transfer everything to a baking dish, top with extra cheese and the buttered panko, and bake at 375 degrees F for 15 to 20 minutes until bubbly and golden. It is the perfect make-ahead option for holidays and gatherings, since you can assemble it and bake it off when you are ready.

Ways to Customize

This recipe is easy to adapt. Use whatever melty cheese you love in place of the Gruyere, like Gouda, fontina, or mozzarella, and swap in any short pasta shape. Stir in cooked veggies like spinach, peas, or broccoli, or add crispy bacon or shredded chicken to make it a heartier meal. For a little heat, add a pinch of cayenne or a swirl of hot sauce, and for a dairy-free version, use a plant-based milk and dairy-free cheeses. It is also naturally easy to make gluten free with your favorite gluten-free pasta.

Storage and Reheating

Store leftovers in an airtight container in the fridge for up to 4 days. To reheat, warm gently over low heat with a splash of milk, stirring, to bring back the creaminess (the microwave works too, just add milk and stir). The blended squash sauce is also very freezer friendly on its own: freeze it for up to 3 months, then thaw, warm gently, and stir in the fresh cheese and cooked pasta when you are ready to serve. That make-ahead sauce is a lifesaver on busy fall nights.

More Cozy Pasta and Squash Recipes

If you love this, here are more cozy favorites to try:

Frequently Asked Questions

Can you taste the butternut squash?
It adds a subtle sweetness and gorgeous color, but blended with the cheese and Dijon it just tastes like a rich, creamy mac and cheese.

Can you taste the cottage cheese?
No. Blended completely smooth, it melts into the sauce and adds creaminess and protein without any noticeable cottage cheese flavor.

How do I keep the sauce from getting grainy?
Blend the cottage cheese fully, shred your own cheese, and melt it in over low heat.

Can I make it ahead?
Yes. The blended sauce keeps for 4 days in the fridge and freezes for 3 months. Add the cheese and pasta when serving.

Is this a good recipe for kids?
Absolutely. The smooth, cheesy sauce is a favorite with kids, and it is a sneaky way to get in squash and extra protein.

How To Make Butternut Squash Mac and Cheese

The Ingredients

Ingredients and Substitutions

  • Butternut squash – or use canned butternut or pumpkin puree (about 2 cups) to save time.
  • Garlic – a whole roasted head; roasted garlic is milder and sweeter than raw.
  • Cottage cheese – full-fat blends creamiest; Greek yogurt or ricotta can sub.
  • Whole milk – any milk works; use a splash of pasta water or broth to thin.
  • Dijon mustard  – key for balancing the sweet squash; do not skip.
  • Sharp cheddar and Gruyere – or Gouda, fontina, mozzarella, or Parmesan.
  • Short pasta – shells, cavatappi, or elbows; use gluten-free if needed.
  • Smoked paprika and nutmeg – warm seasonings that make it taste rich and cozy.

What You Need

The Steps

  • Prep the squash. Heat the oven to 400 degrees F. Cut the squash in half lengthwise and scoop out the seeds. If it is hard to cut, pierce it a few times with a fork and microwave for 2 to 3 minutes first. Rub the cut sides with 1 tablespoon of the oil, then season with the salt, pepper, smoked paprika, and nutmeg.
  • Roast. Put the squash cut side down on a parchment-lined sheet. Drizzle the garlic head with the remaining oil, wrap it in foil, and set it on the same pan. Roast for 40 to 45 minutes, until a fork slides easily into the squash.
  • Cook the pasta. Boil the pasta in well-salted water until 1 minute short of al dente. Save 1 cup of the pasta water, then drain.
  • Blend. Scoop about 2 cups of the squash flesh into a blender and add 4 to 6 squeezed-out roasted garlic cloves, the cottage cheese, milk, 1/4 cup pasta water, Dijon, lemon, and salt. Blend until completely smooth, about 60 seconds. Add more milk or pasta water a splash at a time until it is the texture of a thick soup.
  • Melt in the cheese. Pour the sauce into a large pot over low heat. Add the cheddar and Gruyere a handful at a time, stirring until melted. Keep the heat low so the cottage cheese does not turn grainy. Taste and add salt, and more Dijon or lemon if it tastes flat.
  • Combine. Add the pasta and stir to coat, loosening with more pasta water until it is glossy and creamy. Serve right away.
  • Optional bake. Add an extra splash of milk, since it thickens in the oven. Transfer to a baking dish, top with extra cheese and the buttered panko, and bake at 375 degrees F for 15 to 20 minutes, until golden.

Recipe Tips

  • Blend longer than feels necessary, which is what makes the sauce silky instead of chalky. T
  • aste before the pasta goes in; the sauce should taste slightly over-seasoned on its own, since the pasta mutes it.
  • Shred your own cheese, as pre-shredded has anti-caking starch that makes the sauce gritty.
  • If it tastes too sweet, add more Dijon, lemon, or Parmesan rather than more salt.
  • Make ahead: the blended sauce keeps 4 days in the fridge and freezes for 3 months; warm gently, then add the cheese.
  • Leftovers: reheat with a splash of milk over low heat, stirring, to bring back the creaminess.
  • I highly recommend lots of cracked pepper & chili flakes for a little spice!
 

This butternut squash mac and cheese is the ultimate cozy comfort food, made a little better for you. Sweet roasted butternut squash and mellow roasted garlic get blended with cottage cheese into an incredibly creamy, velvety sauce, then melted together with sharp cheddar and nutty Gruyere. It tastes rich and indulgent, but it sneaks in vegetables and a boost of protein.

It is the kind of dinner the whole family devours, kids included, and no one guesses there is squash and cottage cheese blended right into the sauce. Cozy, creamy, and secretly wholesome, this is fall comfort food at its best.

Bowls of butternut squash mac and cheese

Butternut Squash Mac and Cheese

Print Recipe Pin Recipe
Prep Time 15 minutes
Cook Time 1 hour
Servings 6
Calories 500

Ingredients

For roasting

  • 1 small butternut squash (about 2 lb, halved lengthwise and seeded)
  • 1 head of garlic (top trimmed off)
  • 2 tablespoons olive oil
  • 1 teaspoon salt
  • 1/2 teaspoon black pepper
  • 1/2 teaspoon smoked paprika
  • pinch of nutmeg

For the sauce

  • 1/2 cup full-fat cottage cheese
  • 1/2 cup whole milk (plus more to thin)
  • 1/4 cup reserved pasta water (plus more to thin)
  • 1 tbsp Dijon mustard
  • 1/2 teaspoon salt (plus more to taste)

To finish

  • 1 lb short pasta (shells, cavatappi, or elbows)
  • 1 1/2 cups shredded sharp cheddar
  • 1/2 cup shredded Gruyere or grated Parmesan
  • optional topping: 1/2 cup panko or crushed croutons with 1 tablespoon melted butter

Instructions

  • Prep the squash. Heat the oven to 400 degrees F. Cut the squash in half lengthwise and scoop out the seeds. If it is hard to cut, pierce it a few times with a fork and microwave for 2 to 3 minutes first. Rub the cut sides with 1 tablespoon of the oil, then season with the salt, pepper, smoked paprika, and nutmeg.
  • Roast. Put the squash cut side down on a parchment-lined sheet. Drizzle the garlic head with the remaining oil, wrap it in foil, and set it on the same pan. Roast for 40 to 45 minutes, until a fork slides easily into the squash.
  • Cook the pasta. Boil the pasta in well-salted water until 1 minute short of al dente. Save 1 cup of the pasta water, then drain.
  • Blend. Scoop about 2 cups of the squash flesh into a blender and add 4 to 6 squeezed-out roasted garlic cloves, the cottage cheese, milk, 1/4 cup pasta water, Dijon, lemon, and salt. Blend until completely smooth, about 60 seconds. Add more milk or pasta water a splash at a time until it is the texture of a thick soup.
  • Melt in the cheese. Pour the sauce into a large pot over low heat. Add the cheddar and Gruyere a handful at a time, stirring until melted. Keep the heat low so the cottage cheese does not turn grainy. Taste and add salt, and more Dijon or lemon if it tastes flat.
  • Combine. Add the pasta and stir to coat, loosening with more pasta water until it is glossy and creamy. Serve right away.
  • Optional bake. Add an extra splash of milk, since it thickens in the oven. Transfer to a baking dish, top with extra cheese and the buttered panko, and bake at 375 degrees F for 15 to 20 minutes, until golden.

Notes

  • Blend longer than feels necessary, which is what makes the sauce silky instead of chalky. T
  • aste before the pasta goes in; the sauce should taste slightly over-seasoned on its own, since the pasta mutes it.
  • Shred your own cheese, as pre-shredded has anti-caking starch that makes the sauce gritty.
  • If it tastes too sweet, add more Dijon, lemon, or Parmesan rather than more salt.
  • Make ahead: the blended sauce keeps 4 days in the fridge and freezes for 3 months; warm gently, then add the cheese.
  • Leftovers: reheat with a splash of milk over low heat, stirring, to bring back the creaminess.
  • I highly recommend lots of cracked pepper & chili flakes for a little spice!
 

Nutrition

Serving: 1gCalories: 500kcalCarbohydrates: 60gProtein: 21gFat: 18g

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Recipe creator, toddler mama & wellness enthusiast. Happy&Full is a blog all about quick and easy recipes for every day living! Eating well (and feeling well) doesn’t have to be complicated or expensive.

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