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Dairy-Free "Cheesy" Spaghetti Squash Casserole

Pureed butternut squash, coconut milk, spices and nutritional yeast give this dairy-free "cheesy" spaghetti squash casserole its creamy texture and savory flavor. Gluten-free and grain-free too.

Course Main Course, Side Dish
Cuisine Dairy-free, Gluten-free, Grain-free
Keyword butternut squash, casserole, dairy-free cheese sauce, spaghetti squash
Prep Time 30 minutes
Cook Time 1 hour 5 minutes
Total Time 1 hour 35 minutes
Servings 6


For the veggies:

  • 4 cups butternut squash cubes
  • 1 Tbsp avocado oil
  • Sea salt and black pepper, to taste
  • 1 medium-large spaghetti squash, sliced lengthwise and seeds scooped out

For the sauce:

  • 1 cup full-fat coconut milk
  • 3-4 Tbsp chicken broth, vegetable broth or water
  • 2 tsp coconut aminos
  • 2 tsp fresh lemon juice
  • 3 Tbsp nutritional yeast, or more to taste
  • 1 tsp onion granules or powder
  • 1 tsp garlic granules or powder
  • 1/2 tsp mustard powder
  • 1/2 tsp paprika

For the topping:

  • 1/2 cup + 3 Tbsp almond flour
  • 1/4 tsp sea salt
  • 2 Tbsp avocado oil or melted ghee
  • Sprinkle of paprika for garnish, optional


For the veggies:

  1. Preheat oven to 375 degrees F. Line a baking sheet with parchment paper and add butternut squash cubes to the pan. Drizzle with the avocado oil and season to taste with sea salt and black pepper. Toss to coat. 

  2. In another pan, place the spaghetti squash halves cut-side down. Add about 1/2" water to the pan. Place both pans in the oven. Bake spaghetti squash 30-35 minutes or until fork tender and bake butternut squash 35-40 minutes.

For the sauce and topping:

  1. Add the roasted butternut squash cubes to the food processor bowl with the coconut milk, 3 Tbsp of broth or water, coconut aminos, lemon juice, onion granules, garlic granules, nutritional yeast, paprika, mustard powder, and sea salt and black pepper to taste. Process until smooth, scraping down the sides of the container with a spatula as needed. Taste and adjust seasoning as desired and add extra 1 Tbsp of broth or water, if needed. Mixture will have a bit of thickness to it, but shouldn't be runny.

  2. Preheat oven to 350 degrees F. Once spaghetti squash has cooled enough, scrape the strands with a fork into a 9x13 pan. Season to taste with sea salt. Then, pour sauce mixture over the spaghetti squash and toss to coat.

  3. Mix the almond flour with the sea salt and avocado oil or melted ghee. Crumble mixture on top of casserole in an even layer. Sprinkle paprika on top, if using and bake in preheated oven for 25-30 minutes.

Recipe Notes

This recipe can also be assembled 1-2 days ahead of time and then baked when ready to serve.


Serve with your favorite protein to make this a complete meal.