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Butternut Squash Mac and Cheese is the epitome of Fall comfort food. The sauce is created by roasting sweet and creamy Butternut Squash and then blending it with three cheeses and seasoning it with nutmeg, smoked paprika and the other herbs and spices. This sauce is mixed together with rigatoni pasta and topped with a crispy sage, thyme and buttery breadcrumb topping. It is baked until it is hot and bubbly and just plain magical.

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I have mentioned in other posts how I mourn the absence of Trader Joes in Montana. I won't go into my usual pity party, but I will get straight to the point in saying that I have been forced to come up with a replacement for their seasonal sellout, Butternut Squash Mac and Cheese. It is ridiciulously delicious and we look forward to it every Fall. But...I have to say...this might be even better! And the good/bad part is that this recipe allows for a much larger portion!
Why You'll Love this Recipe
- Easy Make Ahead Meal- This recipe can be made in advance and kept in the fridge and then baked when you are ready to eat!
- Sneaky Veggies- This is a great way to sneak in some veggies. The butternut squash is packed with fiber and vitamins!
- Freezes well- This is a great meal to keep in the freezer (for up to 3 months) and bring out when you need a little ready made comfort food.
Ingredients...
- Butternut squash- So, fortunately, if you are going to do it, this is probably the most convenient time in history to cook with Butternut Squash! You can truly buy it in any possible form. From fresh, to canned, to frozen, to pre-cut. I can't speak about using canned or frozen forms, but I have cooked with both fresh whole and pre-cut Butternut Squash and I didn't see much of a difference. Both are good options. If you are peeling and cubing it yourself, just make sure you have a good peeler and good, sharp knife. Piece of cake.
- Olive Oil
- Butter
- Flour
- Half and Half
- Nutmeg
- Salt and pepper
- Dry mustard
- Smoked Paprika
- Garlic Powder
- Sharp Cheddar
- Gouda
- Parmesan
- Rigatoni
- Fresh Thyme
- Fresh Sage
- Panko Breadcrumbs

How to Cook Butternut Squash
There are different ways to cook butternut squash. Here are a few methods that work well for this recipe.
Whole Roasted Method
- This technique is incredibly easy and works really well in this recipe. To whole roast butternut squash, preheat the oven to 425ยฐF/218ยฐC. Then, simply poke the squash in about 5 places, then place it in a pan or baking sheet and roast for 1 hour. Let it cool completely and then cut it in half, scoop the seeds out, and then scoop out the roasted butternut squash. Use it in recipes such as this mac and cheese, or butternut squash ravioli, or however you'd like!
Roasted Halves Method
- This method is similar to the whole roasted method in that it is very easy, but it nice because it takes less time. For this, you simply cut off the stem and then cut the squash in half the long way. Be very careful and make sure you have a sharp knife. If you are having trouble cutting it, poke a couple of holes in it and then just pop it in the microwave for 2 minute to soften it slightly. After you've cut it in half, scoop out the seeds. Then use a small knife to score the butternut squash flesh into a cross hatch pattern. Rub it with olive oil and season with salt and pepper. Place the squash cut side down on a baking sheet lined with parchment paper. Roast it in the oven at 400ยฐF/205ยฐC for 30-40 minutes until it is tender and starting to caramelize.
Diced and Roasted Method
- This method takes a little more work to prep, but cooks in about half the time. For this method, preheat your oven to 400ยฐF/205ยฐC. Then start by peeling the whole squash. Once it is peeled, cut the top and bottom off of the squash. Then, slice it in half and remove the seeds. Then cut the squash into about 1 inch chunks. Toss the squash pieces with about 2 Tablespoons of olive oil, a large pinch of salt and a few grinds of pepper. Roast it for about 30 minutes, tossing after15 minutes. It is finished when it starts to brown around the edges and is tender and caramelized.

How to Make Butternut Squash Mac and Cheese
Make the Cheese Sauce
Once the squash has been roasted, it is time to create a roux. Melt the butter in a saucepan. When it is melted, sprinkle in the flour and whisk for about 2 minutes. This will cook the raw flour flavor out.
Next, slowly add the half and half. Whisk the lumps out and simmer it slowly until it is smooth and has thickened slightly.
Make sure you have a large sauce pot that can accommodate the cream mixture, the squash and the pasta. Add the roasted squash to the pot with cream mixture. Add the spices and blend. This is where an immersion blender comes in handy. But you can also blend it (carefully!!) in the blender, or mash it by hand. So with whichever technique you choose, mash the squash into the cream mixture so it is nice and smooth.

Next, remove the pot from the heat and add the cheese. Remove it from the heat because if the mixture is too hot, the cheese will, become, "grainy". That is no good. So, make sure you either turn the heat to low, or take your pot off the heat altogether.
Now it is time to add the cooked pasta! It might seem that there is an excessive amount of sauce. But not to worry, the pasta will soak some of it up and I think you will find that it is just right. At this point, you can call it good and it will be perfectly delicious mac and cheese as is. However, I suggest you keep going. It isn't too much more work, but the end result is worth every bit of it!
Make the Buttery Herb Panko Topping
In a skillet, melt ยผ cup of butter. Once it has melted, add the chopped sage and thyme. Let it sizzle in the butter for about a minute. It will become super fragrant.
Add 1 cup of Panko and stir it occasionally until it is golden brown and toasted. That is all there is to it!



Bake
You can either pour your mac and cheese into a nice, big casserole dish, or you can spoon it into individual serving bowls. Either way is perfectly fine.
No matter how you serve it, top the mac and cheese with the crumb mixture topping so that it is generously covered. Pop it in the oven on 350ยฐ for about 30 minutes. Just long enough for the crumb topping to brown and the sauce to get bubbly.
Remove and let sit for about 10 minutes before you serve. Be aware that this dish holds its heat quite well. So, be careful with that first bite. It never fails to make us yelp. We have yet learn patience with this mac and cheese. It is so hard, but I promise it's worth the wait!
Helpful Tools
Knife
There are only a couple of very important tools that you should have for this recipe. If you are cutting the Butternut Squash yourself, make sure you have a nice, sharp large Chef knife or Santoku. I use Shun knives (like this one) and absolutely love them. I believe they are probably the best investment you can make in your kitchen tools. If you are looking for a very nice gift for someone who loves to cook, I would recommend an 8" or 10" Shun Chef's knife. That was my first real quality knife, and what a difference! I have a whole set of Shun knives now and use them every day.

Peeler
Another important, but small investment is a good peeler. I have tried a whole variety of peelers and my absolute, no contest favorite is the Kuhn Rikon Peeler. It is such cheap fun, and a good peeler in the kitchen is so important! It is another great stocking stuffer, host gift, etc. for a cook in your life (or yourself! ).
Immersion Blender
Also, you will need a way to blend the squash. My brother Greggie gave me my immersion blender one year for Christmas. I love it and use it all the time. If you don't have an immersion blender, I would highly consider getting one.
In this recipe you can certainly blend everything in your blender, but it will take several rounds of blending, as there is quite a bit to blend. (Yikes, Mollie, blend much?! ha!)
You can also mash it by hand with a potato masher, but it's just more work. Trust me when I tell you that immersion blenders are game changers in the kitchen and they are one of those super handy tools that are fairly inexpensive and what's better~ they don't take up much space. It might actually be my favorite "extra" appliance.
Large Pot and Serving Bowls
The other tool you will need is a large stock pot to blend the squash and cheese in. I suppose you will also need some individual oven proof serving bowls, or a larger casserole dish. That should just about do it!

Frequently Asked Questions
Well, as mac and cheeses go, it is a healthier option as it is a sneaky way to get more veggies into your meal. Butternut squash is full of vitamins and minerals. It has a ton of vitamin A, vitamin C, and even some protein. So, I will just leave that right there and let you decide. ๐
While, you can use pre-shredded cheese if it is all you have, it is preferable to shred the cheese yourself. Pre-shredded cheeses contain starch or anti-caking agents that prevent the cheese from clumping in the bag. These ingredients also prevent the cheese from melting together smoothly and can create a graininess that is not desirable when you want a smooth, creamy cheese sauce.
Sure! Feel free to change it up, just keep in mind that some cheeses melt better than others. Some of the best melting cheese alternatives to use in this recipe are Fontina, Monterey jack, American, and Pepper Jack.
Yes! Feel free to use a different pasta shape, such as penne, shells, or traditional elbow macaroni.
More Pasta Recipes
- Simple Fresh Pasta Dough- Learn how to easily make your own pasta dough!
- Lemon Pesto Pasta- This light and delicious recipe is fresh and good and so easy!
- Rigatoni with Creamy Mushroom Marsala- The ultimate comfort food pasta recipe. Rich and creamy and so good.
- Orzo Pesto Salad- The lightest and freshest pasta salad you've ever had! Simple and delicious.
- Basic Basil Pesto- Not technically a pasta recipe, but a delicious and simple pesto recipe that is good on any pasta dish. A must have recipe for your recipe box.
I hope you love this delicious pasta recipe. I would love to hear from you in the comments below! Thank you and thank you for visiting Mollie in Montana~*!โฅ๏ธ
๐ Recipe

Butternut Squash Mac and Cheese
Equipment
- 1 lined baking sheet
- 1 Immersion blender or vitamix
- 1 Saucepot
- 1 Baking dish, or individual oven proof bowls
Ingredients
- 2 lbs Cubed Butternut Squash Or 5 Cups
- 2 Tbl Olive Oil
- ยผ Cup Butter
- ยผ Cup All Purpose Flour
- 3 Cups Milk or Half and Half
- ยฝ teaspoon nutmeg
- 1 tsp. salt
- ยผ tsp black pepper
- 1 teaspoon dry mustard
- ยฝ teaspoon smoked paprika
- ยฝ teaspoon garlic powder
- 2 Cups Shredded Sharp Cheddar (shred it yourself)
- ยฝ Cup Shredded Gouda (shred it yourself)
- ยฝ Cup Grated Parmesan
- 1 lb. Rigatoni
Buttery Panko Breadcrumbs
- 1 Tbl Chopped Fresh Sage
- 1 teaspoon Chopped Fresh Thyme
- 1 cup Panko Breadcrumbs
- ยผ cup Butter
- ยฝ teaspoon Sea Salt
Instructions
- Cook Pasta according to directions on package then set aside.
- Placed cubed butternut squash on lined baking sheet.
- Toss with 2 Tablespoons Olive Oil, salt, pepper and nutmeg.
- Bake at 400ยฐf for 30 minutes or until squash is tender.
- Reduce oven temperature to 350โ.
- Melt ยผ Cup Butter in large sauce pot.
- Whisk ยผ cup Flour into melted butter. Cook the flour and butter for 2 minutes until there are no lumps and it smells nutty.
- Slowly whisk in 3 cups half and half or milk. Whisk it until there are no lumps.
- Add cubed butternut squash to half and half mixture.
- Turn off the heat and use immersion blender to blend the squash into a smooth mixture. You can also blend it in a high powered blender, or mash it by hand.
- Add the 3 cheeses as well as dry mustard, smoked paprika, garlic powder, salt and pepper. Stir until cheese is melted.
- Gently stir the sauce into the cooked pasta and then set aside.
- Spoon Butternut Squash Mac and Cheese into oven proof bowls or large casserole dish.
- Top with buttery panko breadcrumb topping (see recipe below).
- Bake in oven at 350ยฐ for 30 minutes until topping is golden brown and bubbling.
- Let sit about 10-15 minutes before serving. It will be VERY HOT!
- Enjoy!
Buttery Panko Breadcrumb Topping
- Melt ยผ cup butter in skillet.
- Add chopped sage and thyme to butter and cook for about 1 minute.
- Add panko to butter and sage and thyme and stir to combine remove from heat.
- Spoon Butternut Squash Mac and Cheese into oven proof bowls or large casserole dish.
Notes
Notes
- While you can use pre-shredded cheeses, I recommend that you shred it yourself. Pre-shredded cheeses contain an anti-caking agent that can cause the cheese sauce to be gritty.
- You can freeze any leftovers in a snap top container. Just thaw it in the fridge the night before you are ready to eat it so it has time to thaw. It is very dense when it freezes and takes a while to thaw all the way.ย
- feel free to add diced chilis or jalapeรฑos for a little kick!
- You can change up the cheeses if you'd like. Some other cheeses that work really well in this recipe are, Monterey Jack, Pepper Jack, American, or Fontina.





Melissa says
I too love the Trader Joeโs butternut squash mac & cheese. Looking forward to making your delicious recipe.
mollieinmontana says
Thank you Meliss! I hope you love it as much as TJ's! ๐
Chris says
TJs doesn't hold a candle this, jump seat your butt out there before Travis eats it all.
mollieinmontana says
Ha! Thanks Chris! Trav is definitely my official taste tester and he approves! ๐