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This Broccoli "Cheese" Spaghetti Squash Bake is a great way to celebrate fall comfort food with none of the guilt! With a cheese sauce made from butternut squash this is Paleo and Whole30!

Broccoli “Cheese” Spaghetti Squash Bake

  • Author: Kelsey


  • 10 cups peeled and chopped butternut squash (about ½ inch cubes)
  • 1 tablespoon avocado oil
  • ½ teaspoon salt
  • ½ cup nutritional yeast
  • ½ cup full fat coconut milk
  • ¾ cup chicken stock
  • 1 teaspoon dijon mustard
  • 1 teaspoon garlic powder
  • 1 teaspoon onion powder
  • Salt and pepper to taste
  • 4 cups broccoli florets (cut them into smaller florets, if you have a big ones, cut them in half!)
  • 1 cooked spaghetti squash (see below for cooking options)


  • Preheat oven to 425 degrees and line a baking sheet with parchment paper.  Place chopped butternut squash on the baking sheet and toss with avocado oil and salt.  Roast for 30-35 minutes or until a fork can easily pierce through the chunks.
  • Place cooked butternut squash in a high powered blender or food processor with nutritional yeast, coconut milk, chicken stock, dijon mustard, garlic powder and onion powder.  Blend on high until smooth then season with salt and pepper to taste.
  • Place both broccoli florets and cooked spaghetti squash strands in a large bowl and pour “cheese” sauce on top.  Toss well to coat everything with the sauce.  Pour the mixture into a 9 x 13 inch casserole dish and place back in the oven for 20-25 minutes.


Ways to cook your spaghetti squash:

  • Instant Pot: Slice your spaghetti squash in half  the short way and remove seeds. Place 1 cup of water in your instant pot then place the grate inside.  Add the spaghetti squash, close the top, place it on sealing and turn it on manual for 6 minutes.  Then once the timer is up turn the venting on to manually vent.
  • Microwave
  • Slow Cooker
  • Roasting