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This easy fall-inspired Baked One Pan Butternut Squash Macaroni and Cheese is rich, creamy, and made all in one pan! With quick cooked fresh butternut squash, plenty of cheese, and caramelized onions- this flavorful mac is a dinnertime fave!

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Easy, creamy and delicious One Pan Butternut Squash Macaroni and Cheese

A decadent, indulgent dish with fall written all over it! This Butternut Squash Macaroni and Cheese with Caramelized Onion is HEAVEN.

If you’re looking to go off the beaten mac and cheese path, look no further. This roasted butternut squash and caramelized onion version of the classic dish adds fall flavor and veggies, but keeps things EXTRA cheesy. The key to making this dish a breeze is prepping ingredients while your butternut squash cooks.

baked Butternut squash macaroni and cheese

Cooking the butternut squash

To cook the squash, you’ll cut it in half lengthwise, and remove the seeds and guts. Then it’s off to the microwave for about 20 minutes, until it’s easily pierced with a fork.

Pro Tip:

Start cooking the squash in the microwave first. This way, it will not only cook, but have time to cool as you prepare the caramelized onions and cook the pasta.

caramelized onions

Caramelizing the onions

If you’ve looked around the blog- it’s no secret that I am mildly obsessed with caramelized onions. I make them in the same fashion as I do in some of my other recipes for this dish- with butter, wine and sugar. With a bit of patience, the onions are a gooey, golden brown masterpiece.

If you love caramelized onions as much as I do- give my Schnitzel Burgers, or Curried Sweet Potato and Lentil Wraps try!

cooking the pasta

Cooking the onions and pasta

The base of the sauce for the One Pan Butternut Squash Macaroni and Cheese starts with caramelized onions. Once the onions are ready, you’ll add the evaporated milk and noodles right to the pan and cook until just under al dente. Be sure to stir the pasta occasionally to prevent it from sticking.

adding the squash

What goes into the Butternut Squash Macaroni and Cheese?

  • 1 medium butternut squash, halved, seeds removed. This will cook in the microwave as you prepare the other ingredients!
  • 1 lb medium shell pasta. You could use any shape you like- this is my fave!
  • Butter.
  • A couple medium yellow onions, diced.
  • Sugar, for caramelizing the onions.
  • Dry white wine or water (for deglazing). I prefer a Sauvignon Blanc or Chardonnay.
  • 3 cans of evaporated milk. These give a rich sweetness, and cook the pasta.
  • Fresh grated nutmeg. SO much better than the dried stuff!
  • Dry mustard powder, for a little zip.
  • Sharp cheddar cheese, for the sauce and topping. Grate yourself for best results.
  • Softened cream cheese, cut into small cubes. Softening and cutting it helps it meld seamlessly into the sauce.
  • Grated parmesan cheese, for a salty tang.
topping with cheese

Baking and serving the mac and cheese

 When pasta is cooked turn off the heat and add the cooked squash, cheeses, and spices and mix well. Top with reserved cheddar, cover and bake for 20 minutes. Uncover and bake 20 more minutes, until golden and bubbly.

This mac and cheese would be great as a side dish (here’s looking at you, Thanksgiving), or main course!

Want to save this recipe for later?

If you make my One Pan Butternut Squash Macaroni and Cheese with Caramelized Onion, please be sure to leave me a comment! I would love to hear from you, and value your feedback! Lastly, if you make the recipe and love it, please tag me on Instagram! I love to see your photos!

Looking for more great sides?

Stuffed Pattypan Squash with Rainbow Chard, Walnuts & Goat Cheese

Roasted Carrots and Parsnips with Honey-Thyme Butter

Crockpot Stuffing

Scalloped Sweet Potatoes with Smoked Gouda and Rosemary

Browned Butter Boursin Mashed Potatoes

Rosemary Air Fryer Potatoes

Made this Butternut squash macaroni and cheese recipe? Leave a review and rating below!

One Pan Butternut Squash Macaroni and Cheese

Prep Time20 mins
Cook Time1 hr 20 mins
Total Time1 hr 40 mins
Course: Dinner, Side Dish
Keyword: butternut squash, caramelized onions, macaroni and cheese
Servings: 8


  • 5 quart or larger dutch oven or oven safe pot


  • 1 medium butternut squash, halved, seeds removed 
  • 1 lb medium shell pasta 
  • 4 tbsp butter
  • 2 medium yellow onions, diced 
  • salt and fresh ground black pepper, to taste 
  • 1 tbsp sugar
  • 1 cup dry white wine or water (for deglazing)
  • 3 12 oz cans evaporated milk 
  • 1/8 tsp fresh grated nutmeg 
  • 1/2 tsp dry mustard powder 
  • 8 oz sharp cheddar, shredded , (reserve half for topping)
  • 8 oz softened cream cheese, cut into small cubes 
  • 1/4 cup grated parmesan cheese 


  • Preheat oven to 400 degrees.
Microwave the squash:
    Cut in half, remove seeds, and microwave for 20-25 minutes on high, turning halfway. 

    Caramelized the Onions:
    1. While squash is cooking, caramelize the onions. Add butter to dutch oven and heat over medium heat until melted.
    2. Add the onions, and season with salt and pepper. Toss the onions to combine with the butter, and continue to cook over medium heat, stirring occasionally, until onions are slightly softened and some moisture is released- about 5 minutes.
    3. Add the sugar, stir to combine with the onions and continue to cook on medium heat for 2 minutes.
    4. Deglaze the pan with 3 tbsp wine (or water), and stir.
    5. Cook 3 minutes, stirring occasionally, until liquid is evaporated.
    6. Continue to add wine or water, 3 tbsp at a time to deglaze the pan, making sure to stir and wait for all liquid to evaporate before adding more liquid. Repeat until full cup of wine or water is gone, making sure to stir and wait for evaporation at each interval. Takes approximately 20 minutes total.
    Finish the Mac:
    1. Once the onions are caramelized, add the milk and pasta, stir well.
    2. Bring to a boil, then reduce heat to medium.
    3. Cook, stirring occasionally for10-14 minutes, until pasta is just under al dente. 

    1. When pasta is cooked turn off the heat and add the cooked squash, cheeses, and spices and mix well.
    2. Top with reserved cheddar, cover and bake for 20 minutes.
    3. Uncover and bake 20 more minutes, until golden and bubbly.

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