Mains
Spaghetti squash casserole: the comfort of a baked pasta dish, with no nightshades and no grains
Mains · serves 8 · 1-2-hours
Core AIP · Elimination phase compliant

This casserole gives you the real experience of baked pasta: squash strands standing in for noodles, seasoned beef, soft vegetables, and a deep red sauce built without a single tomato. The trick is the nomato sauce, butternut squash puree for body, cooked beets for that true red color, and a little gelatin to thicken it the way tomato never could. The original cook says her own teenagers could not tell the difference. It is a project worth doing on a day you have some energy: it makes 8 servings and freezes well, so one afternoon in the kitchen buys you several easy dinners later.
There is real nourishment built into this one. The beef brings zinc and iron, both studied for their role in immune regulation and gut-barrier repair. The butternut squash and beets carry vitamin A and color-rich plant compounds, and the gelatin adds a small dose of collagen, the same kind of gut support bone broth is known for. This is comfort food that happens to be doing quiet work for you.
Source the beef from an animal raised well. If a flare leaves your wrists sore, roast the whole spaghetti squash instead of cutting it raw, a gentler way in. When the casserole comes out of the oven, let it rest a few minutes, then look at it before you serve: the red sauce, the golden strands, the herbs. Take one breath, and bring a calm body to the table.
Ingredients
Base:
- 4 cups cooked spaghetti squash strands (about 1 medium squash)
- 1 lb ground beef
- 1 tbsp coconut oil
- 1 tsp sea salt
- 1 1/2 cups diced onion (or celery, parsnip, or turnip for low-FODMAP)
- 1 cup diced carrot
- 2 garlic cloves, minced
- 3 tsp herbes de Provence
- 1/4 cup water
- Three 4 oz cans mushrooms, drained (or 12 oz fresh mushrooms, sliced and sauteed)
Nomato sauce:
- 1 can butternut squash puree (or about 1 3/4 cups homemade)
- 1/2 cup full-fat coconut milk
- 3 tsp sea salt
- 1/2 cup cooked diced beets
- 3 tbsp gelatin (beef or pork, skippable for a runnier sauce)
Method
Heat the oven to 400F. If you have not already cooked the spaghetti squash, roast it whole or halved until tender, then scrape the strands into a large bowl.
Warm the coconut oil in a large pan over medium heat and brown the ground beef with 1 teaspoon salt. Set the beef aside. In the same pan, add the onion, carrot, garlic, herbes de Provence, and water, cover, and simmer about 10 minutes until the vegetables soften.
For the sauce, blend the butternut squash puree, coconut milk, 3 teaspoons salt, cooked beets, and gelatin until smooth. The beets pull the color toward red and the gelatin gives it the body of a real tomato sauce. For a simpler stovetop nomato marinara you can use on other dishes, see AIP nomato marinara.
In the large bowl, combine the spaghetti squash strands, the beef, the softened vegetables, the drained mushrooms, and the nomato sauce. Fold everything together, then spread it into a large baking dish, about 11 by 15 inches, or several smaller pans.
Bake 30 minutes at 400F, until hot through and lightly set. Let it rest a few minutes before serving. To freeze, bake first, then cool, freeze, and later thaw slowly and reheat.
Instant Pot variation
You can use the Instant Pot to cook the spaghetti squash and brown the beef before assembly, since the casserole itself finishes in the oven. Add a cup of water and a trivet, set the halved squash on top, and cook on high pressure for about 7 minutes with a quick release, then scrape the strands. Use Saute in the same pot to brown the beef and soften the onion, carrot, and garlic. Assemble with the blended nomato sauce and mushrooms, then bake as above. The squash pressure time is a sensible estimate and is flagged for kitchen testing.
*Adapted from asquirrelinthekitchen.com*
Nutrition
Estimated per serving (serves 8), calculated from the ingredients. Actual values vary with brands, sizes, and how much sauce or dressing you use.

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Further reading
Daniela Hess, MSEd, is a co-founder of Great Energy and an Autoimmune Educator and Functional Wellness Consultant who lives and thrives with Hashimoto’s. She is not a licensed medical provider.
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Words in this recipe you can look up. Tap or click a term to learn what it means.
Bone brothCollagenFlareGelatinInstant PotNomatoParsnipSauteSpaghetti squashVitamin AZincEvery ingredient in this recipe is on the Core Autoimmune Protocol food list.
Download the Core Food List (PDF) Explore the food list