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Butternut Squash Macaroni and Cheese with Caramelized Onion

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


  • 1 medium butternut squash, cut into roughly 1”cubes
  • 1 tbsp olive oil
  • salt and fresh ground black pepper, to taste 
  • 2 cups dry elbow macaroni noodles 
  • Cooking spray

Caramelized Onions

  • 2 tbsp butter
  • 2 medium white or yellow onions, sliced thinly 
  • salt and fresh ground black pepper, to taste 
  • 1 tbsp sugar
  • 1 cup white wine or water (for deglazing)

Cheese Sauce

  • 2 tbsp butter
  • 1 tsp minced garlic 
  • 2 tbsp all-purpose flour 
  • 10 oz sharp cheddar, shredded 
  • 4 oz cream cheese, cut into small cubes 
  • 2 cups half and half 
  • 1/8 tsp nutmeg 
  • salt and fresh ground black pepper, to taste 
  • 1/4 cup grated parmesan cheese 


  • Roast the squash
    1. Preheat oven to 425 degrees.
    2. Peel and cut squash into roughly 1” cubes. Place cubes into a large mixing bowl and drizzle with 1 tbsp olive oil and season with salt and pepper.
    3. Transfer to a parchment-lined baking sheet and roast for 40 minutes, flipping halfway through.
    4. Allow squash to cool, and mash with a fork. Once squash is finished roasting, reduce oven temperature to 350 degrees.
    1. While squash roasts, boil 2 cups of elbow macaroni noodles in salted water to al dente, according to package directions. Drain and set aside.
    Caramelized Onions
    While squash is roasting and noodles are boiling, make the caramelized onions.
    1.Peel the onions and slice them in half, and then into thin slices.
    2. Add butter to a large cast iron skillet or non-stick pan, and heat over medium heat until melted.
    3. Add the onions, and season with salt and pepper.
    4. 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.
    5. Add the sugar, stir to combine with the onions and continue to cook on medium heat for 2 minutes.
    6. Deglaze the pan with 3 tbsp of the white wine (or water), and stir. Cook 3 minutes, stirring occasionally, until liquid is evaporated. 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. Once the onions are caramelized, mix in the cooled butternut squash, then remove the mixture to a bowl and set aside.
    Make the cheese sauce and bake the Mac and cheese
    1. Using the same pan you caramelized the onions in, make the cheese sauce.
    2. Add butter to the pan, and heat over medium low. Cook until melted and bubbly, then add garlic and cook until fragrant- about 1 minute.
    3. Add the flour and stir until fully combined. Cook, stirring constantly for 2 minutes over medium-low heat.
    4. Slowly whisk in the half and half and cook, stirring frequently, until thick and bubbly- about 5-6 minutes.
    5. Add the fresh grated nutmeg, salt and pepper to taste and cream cheese cubes and cook, stirring constantly, until cheese is fully melted- about 2 -5 minutes. (Time varies depending on temperature of cheese. Softened cheese will melt faster)..
    6. Once the cream cheese is fully incorporated, turn off the heat and add the fresh grated cheddar cheese. Stir until fully incorporated.
    7. Add the cooked noodles and half the mashed butternut and caramelized onion mixture to the pan.
    8. Pour the Mac and cheese into a cooking spray greased 9x12 glass or ceramic baking dish and top with remaining butternut and onion mixture. Sprinkle the top with grated parmesan and transfer to the oven.
    9. Bake for 30-350 minutes at 350 degrees, until golden and bubbly.
    10. Allow to cool before serving. Sprinkle with finely chopped fresh sage or basil leaves, if desired.