This cheesy garlicy keto spaghetti squash casserole is a great side dish that is bursting with flavor and sunny color. The garlic, parsley, and cheese combination goes deliciously with meatballs or any italian meal.  While winter squash is higher in carbohydrates for a vegetable, this keto casserole still only logs in at 4 g of carbs per serving, and can fit into most people’s low-carb and keto diets.

What is the keto diet? It’s a low-carb, moderate protein, high fat diet that puts your body in fat burning mode rather than carb-burning mode. In addition to helping with weight loss, it also calms and supercharges the brain! Learn more about the keto diet by clicking here.

GAPS Notes: 

Fresh mozzarella is not aged, and therefore not allowed on the GAPS diet.  Aged cheese is allowed, though just ‘mozzarella’ is called out as being not allowed on GAPS.  If you’d feel more comfortable, you can choose to replace the mozzarella with white cheddar in this dish.

What is the GAPS Diet? It’s a gut-healing diet that specifically targets the gut-brain connection to help mental illness and neurological conditions. You can learn more here.

Vegetables on the keto diet

Vegetables provide so much flavor, texture, vitamins and minerals, and variety on the keto diet.  This keto spaghetti squash casserole is a perfect example of how vegetables replace grains with lower carbs and more nutrition! Since those on the keto diet are used to less sugar, you’ll be surprised at how sweet this fun and delicious squash tastes.

Cheesy Spaghetti Squash Casserole

Prep Time: 20 minutes
Cook Time: 30 minutes
resting time: 15 minutes
Total Time: 50 minutes
Servings: 8 servings
Calories: 114 kcal
Spaghetti squash can be served as a yummy cheesy casserole


  • 1 small spaghetti squash 4-5 lbs, yields 5 cups cooked squash
  • Cooking Spray
  • 2 cloves garlic crushed (or more to taste)
  • 2 tablespoons dried parsley
  • 1 teaspoon sea salt if stock is unsalted
  • 1 cup chicken or beef stock
  • 2 cup mozzarella shredded
  • 1/4 cup parmesan cheese shredded


  1. Prepare your spaghetti squash al dante using the method of choice below.
  2. Preheat oven to 375* F
  3. Use a fork to scrape out the flesh into spaghetti strands into a medium mixing bowl. Since we’re baking this casserole in the oven, it’s okay if your squash strands are a little firm.
  4. Spray with cooking spray or use butter or coconut oil to grease a 2 to 3-quart casserole dish that has an oven-proof lid (alternatively, use foil to cover).
  5. Add garlic, parsley, sea salt, half the mozzarella and the parmesan cheese to the spaghetti squash in the mixing bowl. Mix well, until throughly combined.
  6. Place the spaghetti squash mixture in the prepared casserole dish and pour stock over it. Top with remaining 1 cup mozzarella cheese.
  7. Cover casserole dish with lid, and bake on the middle rack for 30 minutes, or until heated through. Remove lid for the last 10 minutes of cooking.
  8. Allow to stand for 15 minutes before serving.
  9. This dish can be prepared ahead of time and kept covered, in the refrigerator, for up to 3 days. If cooking from chilled, increase cooking time to 45 minutes.

To cook spaghetti squash:

  1. Cut spaghetti squash in half crosswise (be careful!) using a large knife. Use a large spoon to scrape the strings and seeds, reserving if desired for roasted squash seeds.
  2. Squash is done when it slightly gives and can be pierced with a fork, but is not mushy. Mushy squash still tastes good, but it won’t have the defined spaghetti strands that are so unique in this casserole. It will continue to cook a bit as it cools.

Instant Pot:

  1. Fill pot with 2 cups of water (use the lines on the side of your pot), place a trivet or steamer basket in, and place squash cut-side down on the trivet or steamer basket in the Instant Pot.
  2. Depending on the shape of your squash and size of your Instant Pot, you may need to do two batches to get the whole squash cooked - no worries, this is a very fast method and you’ll have them both done in no time! If you can fit them both in and still close the lid, you can do both halves at once.
  3. Close the lid, and set the vent to seal. Set the Instant Pot to Manual - 8 minutes* and allow to come to pressure. Naturally let the pressure come down for 5 minutes after it is done cooking, and then use quick release to release the rest of the pressure. Set squash aside to cool until comfortable to touch (15 minutes) before proceeding with the recipe.
  4. If necessary, repeat with the other squash half.

    *Instant Pots can take some getting used to. If your spaghetti squash is too soft after the 8 minutes on pressure and 5 minutes natural pressure release, yours might run a little hot. In contrast, if it is still firm, even after the 15 minutes of cooling, it might run a bit low and you’ll want to add a minute or two to the cooking time for most recipes.

    Finally, if your squash is barely cooked at all, you probably need to replace the silicone ring around the lid. I replace mine about once a month when I’m using the Instant Pot on a daily basis.

    This modern gadget can save oodles of time in the kitchen, but it does take some patience to get it to work how we want it to.

Slow cooker:

  1. First, check to make sure your squash fits in the slow cooker! You can cut it into large ‘rings’ instead of just in half if necessary to make it fit. By keeping it cut crosswise, we get longer squash ‘noodles’ so try to avoid cutting it lengthwise.
  2. Pour 1 cup of water into the bottom of a slow cooker. Place squash cut-side down in the slow cooker and cook on low for 4-5 hours or high for 2 hours.
  3. Open lid and turn off slow cooker and allow squash to cool until comfortable to touch (15 minutes) before proceeding with the recipe.

Oven Roasted:

  1. Preheat oven to 400* F.
  2. Optionally, brush squash ends (cut side) with olive oil, melted butter, or coconut oil. Place cut-side down in a casserole dish or baking sheet *with sides* to contain juices. Add 1 cup of water.
  3. Place squash in the oven (it’s okay if it hasn’t completely preheated yet) and bake for 45 minutes.
  4. Remove from the oven and allow squash to cool until comfortable to touch (15 minutes) before proceeding with the recipe.

Recipe Notes

*If you’re in a time crunch you can put the whole squash in the slow cooker or oven, with the 1 cup of water.  in the oven and slow cooker directions The soft warm squash will be slightly more difficult to work with at the end (be careful- the inside is steaming-hot), but it’s really not much harder to remove the pulp gently after cooking. I do this sometimes when I know I need to get dinner started, but I have something else competing for my attention.

Nutrition Facts
Cheesy Spaghetti Squash Casserole
Amount Per Serving (1 serving)
Calories 114 Calories from Fat 63
% Daily Value*
Fat 7g11%
Saturated Fat 4g20%
Cholesterol 24mg8%
Sodium 633mg26%
Potassium 106mg3%
Carbohydrates 4g1%
Sugar 1g1%
Protein 7g14%
Vitamin A 275IU6%
Vitamin C 3.9mg5%
Calcium 198mg20%
Iron 0.5mg3%
* Percent Daily Values are based on a 2000 calorie diet.

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