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Butternut Squash Macaroni and Cheese

I think the moment I realized it was fall was when I cut into my first butternut squash of the season and the absolute shocking, but gorgeous, Halloween-orange color was revealed. Somehow, the color had faded in my memory since last winter; but take a look at it now– it’s absolutely glorious. It practically screams “Vitamins! Nutrients! Good stuff!”

Or maybe I realized it was fall when I had to run back inside two days in a row to grab a jacket before heading off to work . . . or perhaps it was when I realized I was craving a stick-to-my-ribs dish for dinner. In summer I can get away with something light, but the chill in the air now calls for sterner stuff.

 I’ve combined two of my favorite comfort foods – mac and cheese, and roasted butternut squash. I love how the butternut squash adds tons of Vitamin A and C, along with extra creaminess and its bright orange color, to the sauce. The delicious Hodgson Mill Whole Wheat Elbow Macaroni (Or Gluten-Free Brown Rice Elbows, if you prefer) are much more robust and better for you than regular white flour pasta elbows, and they really grab onto the cheesy, creamy sauce. It’s truly a feast for all the senses.

I got to go home and cook for my family a little while ago, which is always a treat, so I made this dish for them. (Thanks family guinea pigs!) The adorable stunt baby here is my niece, Camdynn. I wish I could take her home with me.

Let’s talk timing. You can either cook this recipe from start to finish, which takes about an hour and a half with roasting the squash, or else you can prep for this recipe a day or two in advance. You can roast the squash up to three days ahead and then refrigerate until you need it. You can also grate the cheese ahead of time and keep refrigerated in an airtight container (or buy pre-grated cheese, if you don’t like grating, of course). When all the ingredients are ready, it takes just 20-25 minutes to cook the pasta, finish the sauce, and bring it together.

I always grate plenty of extra cheese at home to allow for cheese thieves. Cheese thievery is like a sport in my family.

. . . But who could get mad at a cheese thief this cute?

When the squash is roasted and cheese is ready, and I’m ready to start the dish for real, then I like to cook the pasta first, drain, and keep covered to keep it warm and soft until the sauce is done. Just follow the cooking directions on the package. Once cooked, reserve a cup of pasta water for use in making the sauce.

Making the sauce is my favorite part. At first I was intimidated, but now I love making a stovetop cheese sauce. If you’ve never made your own, give it a try. Once you make it once or twice, you’ll start to recognize the stages and doneness, and it’s really, really gratifying to gain that confidence.

While the pasta is cooking, scoop out the roasted and cooled butternut squash, and give it a quick beating with a mixer to make it smooth and remove any long strings. Then add in some good yogurt (I used Greek; plain regular works, too) and blend until smooth again.

On a stovetop, heat some butter and add flour slowly, stirring. It smells delicious, like buttered toast, and gets nice and thick and bubbly.

Slowly add milk, stirring and simmering over low heat until it thickens again. Sometimes you get some lumps, but if you keep stirring they disappear as the mixture thickens. Once it has thickened, add the grated cheese and stir until melted . . .

Finally, add the squash mixture, and stir it all over heat until it’s completely smooth, thick, and bubbling. It’s going to be pretty thick, but eventually it all melts together. Add a little of the pasta water, reserved from cooking the elbows, to thin the sauce while keeping it flavorful. Stir again until smooth. The finished sauce should be thick but pourable.

Then add the finished sauce to the cooked pasta, and mix it up. Use more pasta water if you have to thin it a little more to coat the noodles.

I like to top my bowl of mac & cheese with a sprinkle of extra grated parmesan and sweet, acidic last-of-the-season tomatoes, and sometimes with some toasted walnuts instead of breadcrumbs. I decided to forego the extra step of baking this dish as a casserole – I do love melting more cheese on top for a crust, but I have such fond memories of scooping mac and cheese straight from the pot that I decided to walk down memory lane. (Plus, it’s one less dish to clean.)

Fall has officially arrived! What comfort foods are you making or craving?

Butternut Squash Macaroni and Cheese


  • ½ pound Hodgson Mill Whole Wheat Elbow Macaroni* (1/2 box)
  • 1 ½ cups roasted butternut squash (1 small butternut squash)
  • 2 Tablespoons vegetable oil, such as grapeseed or canola, for roasting squash
  • 1 ¼ cup milk
  • 1 cup plain yogurt (Greek or plain, regular yogurt)
  • 2 Tablespoons butter
  • 2 Tablespoons Hodgson Mill Naturally White Flour*
  • 1 cup shredded parmesan cheese
  • 1 ¼ cup sharp cheddar cheese, grated (6 oz.)
  • 1 teaspoon salt
  • ½ teaspoon pepper
  • ¼ teaspoon dried sage
  • ½ teaspoon paprika
  • 1/4 – 1 cup pasta water, reserved after cooking elbows (amount will vary)

*see notes for gluten-free options

Optional toppings
½ – ¾ cup chopped walnuts, toasted (pecans or hazelnuts are also good)
¼ -½ cup Parmesan cheese
½ – 1 cup cherry tomatoes
Chopped fresh parsley

Cut butternut squash in half and scoop out seeds and strings. Spear several times with a fork, and coat entire squash (outside skin and open faces) lightly with vegetable oil. Roast at 400°F for 45 minutes, or until easily speared with a fork. Allow to cool.

Put salted water for pasta on stovetop to boil. When at a rolling boil, add elbows and cook 7 minutes, stirring occasionally. Drain, reserving 1 cup pasta water for sauce, just in case (You probably won’t need quite that much.). Don’t rinse pasta; return to pan or bowl and keep covered and warm.

Scoop out cooled butternut squash. Measure out 1 ½ cups of cooked squash, and using a mixer, blend this with 1 cup Greek yogurt and spices (salt, pepper, paprika, sage) until smooth.

In a large skillet over medium-low heat, melt butter, then add flour and stir until thick, bubbling, and browned. It will smell baked, like buttery bread. Turn heat to low. Slowly add milk, stirring until it’s combined and smooth. (Use a whisk if it won’t hurt your pan, but use a wooden or plastic spoon if your pan is nonstick). Bring to a simmer and keep stirring until it thickens. Lumps should go away as long as you keep stirring as it thickens.

Add grated cheese and stir until completely melted and bubbling. Then add butternut squash/yogurt mixture and cook until all is smooth and bubbling. Mixture will be thick. Add pasta water if needed to thin it down. Start with ¼ cup, and add more if mixture is too thick to pour.

Add cheese and squash mixture to elbows and stir until coated. Add more pasta water if needed to help cheese sauce coat the noodles. Serve hot. Topping suggestions: extra grated parmesan cheese, fresh parsley, toasted walnuts, flavorful grape or cherry tomatoes.


Keeps for up to 3 days in sealed container in fridge. Makes great left-overs. Heat in microwave or in pan over very low heat, stirring constantly.Gluten-free option: Use Hodgson Mill Gluten-Free Brown Rice Elbows, and replace flour with Hodgson Mill Gluten-free Seasoned Coating Mix.


Makes 6-8 servings.

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Author: Erin

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Showing 2 Comments
Avatar  prov31wannabe 5 years agoReply

What, no comments on that cutey patooty Camdynn and her wonderful mother? (Sorry, should I be omitting names to protect privacy?) Can't wait to try this! We have squash! Would you believe I have never made mac & cheese from scratch. It's Kraft Dinner all the way for us!

Avatar  Erin 5 years agoReply

I know- with those cheeks, she could take the baby modeling world by storm!

I hadn't made mac & cheese from scratch either before getting this idea and trying out various recipes. It was certainly edifying. I felt good knowing I was using real cheese and whole wheat elbows -- I'm not sure what's in that neon orange cheese powder, even though it's so tasty . . . .

Thanks for commenting! : ) I hope it's a huge success for you (and with your family), and that you tell me how it goes!

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