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butternut squash mac and cheese on a plate

Butternut Squash Mac and Cheese

  • Author: Jenna Barnard
  • Prep Time: 1 hour
  • Cook Time: 30 minutes
  • Total Time: 1 hour 30 minutes
  • Yield: 5-6 servings 1x


This creamy butternut squash mac and cheese is topped with herby and crispy bacon breadcrumbs. It’s also dairy free and gluten free!



Bacon Breadcrumbs

  • 5 oz (46 strips) bacon *see notes for vegan version
  • 2 1/2 cups (120g) gluten free bread (about 5 slices)
  • 2 tsp fresh thyme
  • 4 fresh sage leaves 

Butternut Squash Mac and Cheese

  • 12 oz uncooked gluten free pasta**
  • (1) 2 lb butternut squash
  • 1 tbsp olive oil, divided
  • 4 cloves garlic, roughly chopped
  • 1/2 yellow onion, diced
  • 3/4 cup raw cashews OR sunflower seeds, soaked in water in the refrigerator overnight***
  • 1/2 cup nutritional yeast
  • 1 tbsp + 1 tsp white wine vinegar (lemon juice is also OK)
  • 1 tbsp coconut aminos
  • 2 tsp dijon mustard
  • 1 tsp smoked paprika
  • 1 1/2 tsp kosher sea salt****
  • 1/2 tsp fresh cracked black pepper, or to taste
  • 1/4 tsp ground nutmeg
  • 1 1/4 cups almond milk
  • 1/2 cup reserved pasta water
  • 1 cup shredded vegan cheddar cheese


  1. Preheat the oven to 400F and line a baking sheet with foil.
  2. Cut the butternut squash in half, lengthwise, and scoop out and discard the seeds.
  3. Place the squash cut side up on the baking sheet. Drizzle with 1/2 tbsp olive oil and rub into the surface of each half.
  4. Sprinkle with some salt and pepper and bake for 1 hour, or until fork tender.
  5. Meanwhile, heat a skillet over medium heat and drizzle with the other 1/2 tbsp of olive oil. 
  6. Once hot, add the onion and garlic and sauté until lightly browned and translucent. 
  7. Scoop the onions and garlic into a high speed blender, along with the drained cashews, nutritional yeast, vinegar, coconut aminos, mustard, paprika, 1 1/2 tsp salt, 1/2 tsp pepper, and nutmeg. Do not blend yet, just set aside.
  8. Return the skillet to the burner and cook the bacon until browned and crispy. Transfer to a plate lined with a paper towel and reserve about 1 tablespoon of the bacon grease. 
  9. Next, place the slices of bread in an even layer on a baking pan. Place into the oven with the butternut squash to toasted for 5 minutes on each side. This will make it easier to blend into breadcrumbs. But if your bread is already a stale, you can skip this step.
  10. Cut or tear the bread into bite-sized pieces and measure out roughly 2 1/2 cups to ensure you have the right amount. Add to a food processor along with the bacon, thyme, and sage. Blitz into a fine crumble, then mix in the reserved bacon grease by hand. Set aside.
  11. Now boil your pasta according to the instructions on the box. Once al dente, drain (reserving 1/2 cup of the water) and rinse the pasta with cold water. Pour the pasta into a 2 quart casserole dish and toss in the vegan shredded cheese. Set aside.
  12. By now the squash should be done. After removing, reduce the oven temperature to 375F. Allow the squash to cool, then scoop out the flesh and measure to 2 cups. Add it into the blender with the rest of the ingredients, along with almond milk and reserved pasta water.
  13. Blend on high until smooth. Pour the sauce over the noodles and stir to combine. Sprinkle all of the breadcrumbs on top, in a hefty layer, bake for 25-30 minutes.
  14. It’s ready when the breadcrumbs are a deep golden brown and the edges are barely bubbling. 
  15. Allow the dish to cool for about 10 minutes, then dig in!


  • *VEGAN OPTION – To make this recipe vegan, swap the bacon with mushrooms. Oyster is preferred, but you can use any you like. To make, place a skillet (preferably cast iron) over medium heat and drizzle with a bit of olive oil. Once hot, add the mushrooms. Heat on one side, pressing the mushrooms into the pan, until golden brown. Flip and brown on the other side. Once browned and shriveled, remove the mushrooms and place into a food processor with 1/2 tsp salt. Blitz until ground into small bits, and mix into the breadcrumbs with 1 tbsp olive oil or melted vegan butter.
  • **GLUTEN FREE PASTA – I prefer to use brown rice pasta for this recipe because I find it doesn’t break nearly as easily as chickpea or lentil pasta. But of course, use whichever you prefer or are able to eat! 
  • ***SOAKED CASHEWS – If you didn’t have time to soak the cashews overnight, you can also boil them for about 10 minutes or until tender. But do not skip this step of soaking or boiling, otherwise the sauce won’t turn out as smooth and creamy.
  • ****SALT – Kosher sea salt is coarse, so 1 1/2 tsp of this salt is less than 1 1/2 tsp of standard fine table salt. If you’re using fine table salt, only use 1 tsp and then taste test to see if you need more.

Keywords: butternut squash mac and cheese, gluten free mac and cheese, dairy free mac and cheese, baked mac and cheese

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