
Happy New Year, friends! Let’s kick the year off right with a healthy comfort food recipe: dairy-free “cheesy” spaghetti squash casserole. Are you with me?
This casserole gets its “cheesiness” from roasted and pureed butternut squash, creamy coconut milk, savory spices and nutritional yeast. Gotta love a dose of hidden veggies in sauce, right? And, squash lovers unite because this recipe is squash-on-squash!

Keep in mind, this is not macaroni and cheese — it just isn’t, and isn’t necessarily supposed to be either. But, it does have cheesy qualities like creaminess and umami flavor. The almond flour crumble is similar to buttered breadcrumbs or crackers that are often seen atop of baked mac n’ cheese. But really, this casserole is a special thing of its own and totally delicious. For those of you that miss cheesy flavor, but can’t tolerate cheese, this is especially for you.

I gotta say, this casserole tastes even better the next day — and even better the day after that! The “cheesy” flavor comes out a bit more and everything just seems to be more united.
If you like this recipe and are interested in other ways to use butternut squash as a “cheese” base, check out my dairy-free butternut squash nacho “cheese” dip.
Cheers and enjoy!

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.
- 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
- 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
- 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
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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.
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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.
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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.
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Preheat oven to 350 degrees F. Once spaghetti squash has cooled enough, scrape the strands with a fork into a 9×13 pan. Season to taste with sea salt. Then, pour sauce mixture over the spaghetti squash and toss to coat.
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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.
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.
Does this recipe freeze well?
Hi Karen,
I haven’t tried freezing it, so can’t speak on this firsthand, but imagine it would freeze well. If you try it, let me know how it goes!