If you have been on the hunt for the most creamy, cozy, vegetable-packed butternut squash mac and cheese that actually rivals the Trader Joe's version — this is it. Rich gouda, sharp cheddar, and nutty parmesan come together with a silky pureed butternut squash sauce for a fall pasta dinner that is genuinely one of the best things to come out of my kitchen all season.
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The BEST butternut squash mac and cheese
There is a reason this butternut squash mac and cheese has become one of the most-made fall recipes on ELW — it is the dinner that makes everyone at the table completely silent with the first bite, and then immediately asks for seconds. A velvety pureed butternut squash sauce forms the base, enriched with a triple-cheese blend of gouda, sharp cheddar, and parmesan, and seasoned with nutmeg, mustard powder, and a pinch of cayenne. The result is a pasta dish that tastes completely indulgent while sneaking in serious nutrition from the squash.
What makes this homemade butternut squash mac and cheese so special is the sauce technique — everything cooks together in one pot, gets blended completely smooth with an immersion blender, and then gets finished with three melted cheeses for a sauce so silky it coats every single piece of rigatoni in the most beautiful way. It is the ultimate fall comfort food dinner and honestly one of the best Thanksgiving side dishes you can bring to the table. If you are in a fall cooking era right now, you also need my Butternut Squash Soup and my Fall Harvest Salad in your life — and for more cozy pasta nights, my Spicy Fusilli Pasta and One Pot Chicken Parmesan Pasta are both weeknight staples around here.
Why You’ll Love This Recipe
- Silky smooth butternut squash sauce. The squash gets pureed completely smooth and creates the most luxurious, velvety sauce base — no béchamel, no flour-based roux needed.
- Three-cheese blend. Gouda, cheddar, and parmesan together create layers of flavor that a single-cheese mac can't compete with.
- Sneaks in a full serving of vegetables. Four cups of butternut squash disappear into the sauce and nobody will know they're eating something nutritious.
- One pot from start to finish. Everything happens in the same pot — minimal cleanup for maximum reward.
- Feeds a crowd. Twelve generous servings from one pot makes this perfect for potlucks, Thanksgiving, or a big family dinner.
Ingredients Needed To Make This Butternut Squash Mac and Cheese
Here’s a little bit about everything that goes into this butternut squash macaroni and cheese:
- Rigatoni: One pound of rigatoni is the ideal pasta shape here — the ridges and hollow tubes trap the silky squash sauce inside every bite. Macaroni, penne, or mezzi rigatoni all work beautifully as substitutes. For gluten free, use your favorite GF pasta shape.
- Butternut squash: The star of the show — four cups of peeled and cubed butternut squash. You can peel and cube it yourself or buy it pre-cut from the produce section to save time. Frozen butternut squash cubes also work perfectly.
- Shallots + garlic: Two finely diced shallots and two cloves of minced garlic build the savory, aromatic base of the sauce. Don't skip either — they disappear into the sauce but make a real difference in depth of flavor.
- Butter: Two tablespoons to sauté the aromatics and start building that rich, cozy sauce foundation.
- Chicken or vegetable broth: One and three-quarters cups form the braising liquid that cooks the squash until fork-tender and becomes part of the sauce after blending. Use vegetable broth to keep this fully vegetarian.
- Milk: One cup of whole milk stirred in after blending makes the sauce extra creamy and luscious.
- Gouda: One cup of shredded gouda — mild, buttery, and it melts beautifully into the sauce. Don't skip this one; it's what makes this mac taste different from every other version.
- Cheddar cheese: One and a half cups of freshly shredded sharp cheddar. Always shred your own from a block for the smoothest, creamiest melt.
- Parmesan: Half a cup freshly grated, plus more for topping. Adds that sharp, salty, umami finish that pulls everything together.
- Nutmeg + mustard powder: The two secret weapons. Mustard powder adds a subtle tang that balances the squash's sweetness, and nutmeg adds that unmistakable warm fall depth. Both are non-negotiable.
How to make butternut squash mac and cheese
- Step 1: Cook the butternut squash.
Add the cubed butternut squash to the pot. Season with salt, pepper, mustard powder, nutmeg, and cayenne — stir everything to coat. Pour in the chicken or vegetable broth and bring to a boil. Reduce heat slightly and cook for 8–10 minutes until the butternut squash is completely fork-tender and breaking apart.
- Step 2: Blend until silky smooth. Using an immersion blender directly in the pot, blend everything until completely, perfectly smooth. The sauce should look like a silky, golden velvet. Reduce the heat to medium-low. Stir in the milk, then add the shredded gouda, cheddar, and parmesan in batches, whisking constantly until each addition is fully melted and incorporated before adding the next. The sauce should be thick, glossy, and deeply golden. If it feels too thick, add a splash of the reserved pasta water to loosen it.
- Step 3: Add the pasta and serve.
Add the cooked rigatoni to the cheese sauce and toss until every piece is completely coated. Taste and adjust seasoning — a pinch more salt, a crack of black pepper, or an extra pinch of cayenne if you want more heat. Serve immediately topped with a generous shower of freshly grated parmesan.
Erin's Expert Tips
Buy pre-cut butternut squash. Peeling and cubing a raw butternut squash is genuinely hard work and takes real time. Pre-cut butternut squash from the produce section or freezer aisle is a completely legitimate shortcut that I use myself regularly.
Shred your own cheese. Pre-shredded cheese contains anti-caking additives that prevent smooth melting — you'll end up with a grainy sauce instead of a silky one. A block of cheese and a box grater takes less than two minutes and makes the most dramatic difference.
Don't skip the nutmeg. I know it sounds unusual but nutmeg in mac and cheese is a classic for a reason — it adds warmth and depth that you can't put your finger on but would absolutely miss.
Add cheese over low heat. High heat causes cheese proteins to seize and the sauce to break into a greasy, grainy mess. Keep the heat on medium-low when adding the cheese and whisk constantly.
Try the baked version. Pour the finished mac into a baking dish, top with panko and parmesan, and bake at 375°F for 20–25 minutes. Multiple readers have done this and said it was even more incredible — the crunchy topping is a game changer.
Storage: Store in an airtight container in the refrigerator for up to 4 days. The pasta will absorb some of the sauce as it sits — reheat in a pot over medium-low heat with a splash of milk or broth to bring it back to its creamy original consistency. This dish can also be frozen for up to 3 months in a freezer-safe container, though note that the pasta texture will change slightly upon thawing.
Frequently Asked Questions
Below are some common questions about this butternut squash mac and cheese. Don’t see the answer you’re looking for? Leave a comment at the bottom of this post!
Genuinely yes — and this is not a humble opinion, this is the feedback from readers who have tried both. The homemade version is fresher, more flavorful, and you can customize the cheese blend and seasoning to your exact taste. Several readers have commented that this is better and better for you than the TJ's version they love.
Absolutely — frozen cubed butternut squash works perfectly here and is a great time-saver. Add it straight from frozen to the pot with the broth — you may need to add 3–5 extra minutes to the cooking time to ensure it's fully tender before blending.
Yes — simply swap the pasta for your favorite gluten free shape. The sauce itself is completely gluten free with no roux or flour needed.
A crisp green salad balances the richness perfectly — my Kale Superfood Salad or Fall Harvest Salad are both ideal. For a complete meal, add a protein — grilled chicken, crispy bacon, or roasted sausage are all excellent alongside.
It is one of the best Thanksgiving side dishes you can make — the fall flavors are perfect for the holiday, it serves a crowd, and it can be made almost entirely ahead of time. It always gets more compliments than the turkey.
if you liked this recipe, try these!
Find more cozy, crowd-pleasing pasta and fall recipes right here on ELW:
If you tried this recipe or any other recipes on my blog, please leave a 🌟 star rating and let me know how it went in the 📝 comments below. Follow @erinliveswhole on Instagram and tag me in any of the recipes you make so I can repost them!
Butternut Squash Mac and Cheese
Ingredients
Method
- Heat large pot with water and salt, bring to boil. Cook noodles according to package, drain, and set aside.
- In same large pot, turn heat to medium-high and add butter and shallots. Cook for two minutes and then add in garlic and butternut squash.
- Add all spices, stir, and then add in chicken broth. Bring to boil and cook until butternut squash is tender, about 8-10 minutes. Using a blender or immersion blender, blend until completely smooth.
- Reduce heat to medium-low and stir in milk and all of the cheeses. Use a whisk to help blend. Once cheese is melted, stir in pasta and toss until evenly coated.
- Top with more parmesan cheese and serve! Enjoy!
Nutrition
Tried this recipe?
Let us know how it was!Recipe by Erin Morrissey and Photos by The Mindful Hapa
Taylor Beatty says
Insanely good!! Pretty much a one pot meal which makes cleanup a breeze. Incredible way to get extra veg and so cozy for fall!
Manning says
So easy and so good! Comfort food at its finest.
Erin says
Hi Manning, so happy you loved it! 🙂
Jen says
Delicious!!
Brittany B says
I love the Trader Joe’s butternut squash Mac and cheese, but this is even better and better for me! So delicious
Christina says
Our family tried this for the first time for Christmas and it was a hit! Even my toddlers enjoyed it 🙂 Will definitely be making again!
Erin says
Hi Christina, so happy everyone loved it! 🙂
Katelynn H. says
This recipe is fabulous! It's one of my go-tos in the fall. Do you think it could be made in a crock pot version? I'd love to be able to bring it to work parties where we don't have a full kitchen.
Jennifer Burkhart says
Can you use frozen butternut squash?
Erin says
Hi Jennifer, yep, should be fine. Let me know how yours comes out!
Brittany says
This tastes exactly like the TJ's Butternut Squash Mac and cheese but obviously so much better!
Erin says
Hi Brittany, so happy you loved it!! 🙂
Sam says
This was super easy and delicious! I wanted to make a mac n cheese with a veggie for my 10 month old son and he loved it and so did we. I'm sure Rhys will too 😊
Erin says
Hi Sam, so happy it was a hit!! 🙂
Kelli says
Soooo yummy I added bacon to the top of mine
Erin says
Hi Kelli, so happy you loved it and great idea!! 🙂
Jess L says
Obsessed! This was sooo good & so easy to make. So happy to be able to make my own version of one of my Trader Joe’s favorites!
Erin says
Hi Jess, so glad you loved it! 🙂
Pat says
OUTRAGOUSLY Delicious!!! A co-worker brough this butternut squash mac and cheese in for a Thanksgiving potluck. She made two pans to share -- ALL 20 of us asked her for the recipe........ITS THAT GOOD.
I will be making this for my next party and get together.
Erin says
Hi Pat, so happy it was a big hit! Thanks for sharing!! 🙂
Margaret says
So delicious!! Love that I’m getting vegetables in a serving of “Mac & Cheese”
Erin says
Hi Margaret, so glad you love it! 🙂
Vanessa says
So delicious and makes so much! Whole family loved it and the leftovers tasted just as good the next day.
Erin says
Hi Vanessa, so happy everyone enjoyed it!!
Claire says
Perfect meal for a cozy rainy day!!
Erin says
Hi Claire, so happy you liked it! 🙂
Susan says
This was delicious! I followed Vic’s que and used breadcrumb topping mixed with parmigiano. I also used mezze rigatoni pasta. To us, noodles are flat cut ribbons of different widths that are used for soup, or as a side in Polish and German cooking. Baked at 375 for twenty minutes. I had halved the recipe for just myself and husband, and leftovers. Wonderful!
Erin says
Hi Susan, so happy you loved it and made it your own! Sounds great!! 🙂
Vic says
My entire family LOVED this recipe. It was so easy (especially since I used already peeled and cut butternut squash :D) and delicious. I did put it into a 9x13 pan and baked it for 30 mins at 375 with a breadcrumb topping which made it even more heavenly!
Erin says
Hi Vic, so happy it was a hit!! 🙂
Kerry Kramer says
Was just talking to my friend about how much I love the tj butternut Mac and cheese and then Erin posted this! This was the best meal for the rainy weekend we are having. It was super easy to make and tasted great! I added some dried sage for some more of that fall taste. Next time I definitely want to try some pancetta like she suggested!
Erin says
Hi Kerry, so happy you loved it so much and great idea! 🙂