Best Butternut Squash Mac and Cheese – Instant pot Recipe

This healthier, easy butternut squash mac and cheese is made with all whole ingredients including delicious squash that you can make in under 10 minutes all in the Instant Pot! Enjoy it as a healthy dinner the whole family will love any day of the week. Gluten-Free!

Fall is finally here and I thought I would kick it off with this incredible butternut squash mac and cheese that is so comforting, warm, and packed with such great flavors. 

I made this mac and cheese recipe with butternut squash a while back but I felt like it needed an upgrade. I am happy to tell you that it is made with frozen butternut squash which is great since it eliminates the peeling and chopping. A task that in all truth is not my favorite. 

The addition of the squash gives this mac and cheese a nice creamy taste without adding extra cheese and butter.

You can of course use cubed roasted squash that you peel, cook, and freeze yourself if you are into that. I have plenty of other butternut squash recipes that use fresh squash like this butternut squash lasagna and these butternut squash noodles. 

But in this recipe, we are going to take a nice shortcut from the store and use frozen squash.

Why you’ll love this recipe

• Quick and easy all made in the Instant Pot!
• A healthier mac and cheese recipe that even the kids will love. 
• It only takes 10 minutes to make it!
• Crazy creamy and delicious thanks to the cheese + butternut squash combo.
• The BEST gluten-free mac and cheese!

What makes this mac and cheese recipe healthier?

This homemade mac and cheese recipe is made a little lighter and healthier but is still creamy and packed with flavor.

• Less dairy and butter
• Only 1 cup of cheddar cheese + some salty parmesan cheese.
• Uses gluten-free pasta instead of white pasta
• It has healthy butternut squash to add more fiber and nutrition.

Butternut squash mac and cheese ingredients

Just a few simple ingredients are needed to make this amazing recipe! Here is what you’ll need:

• Frozen butternut squash – store-bought, you could also use fresh peeled, chopped, roasted, frozen squash if that is what you have on hand.
• Pasta shells – I used Banza brand chickpea pasta shells but any type of gluten-free pasta will work. You can even use regular pasta.
• Shredded sharp cheddar cheese – you can shred your own or use store-bought shredded cheese.
• Grated parmesan cheese – make sure it is grated and not shredded since it will melt better.
• Vegetable stock – you can also use chicken stock.
• Coconut milk – full-fat, canned coconut milk. Not beverage coconut milk since it is not as thick and creamy. You can also use heavy cream.
• Shallot – for a kick of flavor
• Garlic – real garlic or garlic paste (about 1 tablespoon) will work.
• Oregano + chili powder – for added flavor.
• Salt and pepper – kosher salt and ground black pepper
• Fresh sage – is optional for the topping but the added flavor is incredible!
• Butter – just a little bit to bring it all together.

How to make butternut squash Mac and cheese in the Instant Pot

It is so easy to make this mac and cheese recipe in the Instant Pot in just 10 minutes! Here is a summary of the recipe with step-by-step photos. Get the complete list of recipe ingredients, instructions, and nutrition in the recipe card located at the bottom of this post.

1. Sauté the onions and garlic. Set the Instant pot to saute and add the oil and butter then add the shallots and garlic and cook until translucent and fragrant. Then stir in the oregano, chili powder, salt, and pepper and cook for 1 minute.
2. Add the pasta and squash. Turn the instant pot to warm then add the stock, water, squash, and pasta. Stir that all together.
3. Pressure Cook. Secure the lid and set the instant pot for 4 minutes on “manual mode” or “pressure”, depending on the type of instant pot you have.
4. Release the pressure. After 4 minutes, do a quick release. Once all of the pressure is released, carefully remove the lid.
5. Add the cheese. Stir in the shredded cheddar cheese, parmesan, and coconut milk. You want to stir it until the cheese fully melts, about 1 minute or so. Then season with more salt and pepper to taste.
6. Serve. Serve warm and top with fresh chopped sage.

This butternut squash mac and cheese is so incredibly cheesy, comforting, and delicious!!!! Try to refrain from eating it all! Lucky for me, the kids ate a ton of it so there wasn’t too much left for me, haha!

Expert tip: Add the liquids (broth and water) before adding the pasta and squash to the pot and give it a good stir before cooking it to prevent any burning on the bottom of the pot. If it does burn a little bit then just stir in a touch of stock or water to deglaze. Plus crispy pasta pieces on the bottom are amazing!

Tips for making this homemade mac and cheese with butternut squash

• Use frozen butternut squash – The extra liquid from the frozen squash helps to cook the pasta. I tried this with regular, cubed butternut squash and it took much longer to cook and was not as smooth and creamy. Besides, nobody wants to sit there and peel and cut squash if it is not necessary, right?
• You can use any kind of pasta, maybe not spaghetti though. I tried this with gluten-free chickpea pasta and regular pasta and both worked great! It would also be wonderful with elbows, rotini, or penne.
• Use full-fat coconut milk – This made all the difference and made this taste so decadent. I always pour my coconut milk into a bowl and whisk it a little before adding it to anything, so it is nice and smooth.
• You want to shred the cheese yourself if you can. Pre-shredded, store-bought cheese just doesn’t melt as well. Trust me! For a quick shortcut, simply cut up a block of cheddar cheese into chunks and throw it in the food processor to shred it up. It’s a great time saver.

Recipe variations

• Add in some veggies like cooked broccoli, cauliflower, or spinach.
• Add in some protein like ground meat, ham, bacon, or chicken.
• Fold in some herbs like thyme, oregano, or chives.
• Use different cheeses like gruyere, white cheddar cheese, or Monterey jack cheese.

What to serve with Mac and cheese

• Serve it up with a Salad. Such as this 10-Minute Chopped Italian Salad or this Kale and Brussel Sprout Salad.
• Some hearty proteins. Such as this Healthy Turkey Meatloaf or these Baked Eggplant Meatballs.
• Enjoy it with some veggies like Brussel sprouts, asparagus or mushrooms.

Storing and reheating

To store: You can store this butternut squash mac and cheese in an airtight container in the refrigerator for up to 4 days.

To reheat: You can reheat portions in the microwave or in a pot on the stovetop.

More butternut squash recipes

• Air Fryer Butternut Squash
• Roasted Butternut Squash Soup
• Mashed Butternut Squash
• Stuffed Butternut Squash

Did you try this butternut squash mac and cheese recipe? If you did, then please leave a rating and comment below. I would love to hear how it turned out!

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