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Last updated December 16, 2022

Baked Spaghetti Squash Casserole (Paleo, Whole30, Keto)

This Paleo & Whole30 Spaghetti Squash Casserole is the perfect weeknight dish that the whole family will love! It’s a healthier, low carb version of your favorite Italian-spaghetti dish. You won’t miss the noodles! Paleo, Whole30, and Keto friendly!

Baked Italian Spaghetti squash in white casserole dish with wooden spoon

Spaghetti Squash Casserole

This baked Italian spaghetti squash casserole has been my favorite! Cooked spaghetti squash combined with a homemade meat sauce that’s baked to perfection. YUM.

I swear it taste exactly like Italian spaghetti, but it’s made with nutritious spaghetti squash, instead of processed pasta noodles.

The best thing about spaghetti squash is that it’s low carb, but filling at the same time. This paleo spaghetti squash casserole is easy to make, healthy, and freezer friendly. The longest part of the recipe is baking the spaghetti squash.

Spaghetti squash and wooden spoon in white casserole dish

Is Spaghetti Squash A Good Carb?

I really don’t like to label foods good or bad, so I’m just going to state the #facts.

Spaghetti squash is a winter vegetable that’s rich in vitamins, minerals, and antioxidants. It also contains a good amount of fiber. For more nutrition info on spaghetti squash, read here.

At the end of the day, spaghetti squash is going to be more beneficial to your health than processed pasta. Spaghetti squash is lower in calories, lower in carbohydrates, and contains more nutrients than pasta (no matter if the pasta is whole grain, whole wheat, etc.)

How To Cut Spaghetti Squash

Making a spaghetti squash seems a lot more complicated than it is (I promise it’s really not). The hardest part is cutting the spaghetti squash.

The outside of a spaghetti squash is extremely tough and even if you are using a sharp knife, you will have to take a strong swing at it.

The easiest way to cut a spaghetti squash is to microwave it before cutting it. This softens the outer shell of the squash making it super easy to cut through and slice evenly. See my tips below:

  • Poke holes in the squash with a fork (just like you would with a potato)
  • Place the squash in the microwave and cook for 3-4 minutes.
  • Take the squash out with oven mitts (the squash will be hot!)
  • Trim the ends off of the squash, and slice evenly in half
  • Scoop out the seeds and stringy parts in the center of the squash using a fork

How To Make Paleo Spaghetti Squash Casserole

  • Bake the squash for 30-35 minutes
  • While the squash is cooking, saute the garlic and onions. Add the ground beef and cook until it’s no longer pink.
  • Add the seasonings, tomato paste, tomato sauce, and diced tomatoes to the skillet.
  • Scrape the squash out of the boat
  • Add squash, and beef skillet mixture to a large bowl. Stir mixture until all the squash is covered.
  • Crack the eggs and stir again.
  • Pour squash into a casserole dish and bake for 25 minutes.
Baked Italian spaghetti squash in white casserole dish

Tips And Variations

  • Sub ground beef with ground Italian sausage, pork, turkey, or chicken. Opt for high quality meats that are grass-fed or pasture raised.
  • If you aren’t able to make homemade meat sauce, use jarred sauce instead. You can use a marinara or pasta sauce. Look for sauces without added sugars, artificial ingredients, gluten, and canola or soybean oil. If you are Paleo or Whole30, look for Paleo-certified, Non-GMO, or Whole30 approved. My favorite sauces are Primal Kitchen Tomato Basil Marinara Sauce, and Rao’s Homemade Marinara Sauce.
  • Store leftovers in an air tight container for up to 5 days in the fridge.
  • To make ahead, roast the spaghetti squash and shred it into a container. Store it in the fridge for up to 3 days, and combine it with the meat sauce when the casserole is ready to be made.
  • Add fennel seeds for a bit of sweetness

Can I Freeze Spaghetti Squash Casserole?

Yes! However the Paleo and Whole30 spaghetti squash may become a little watery when thawed. If you don’t mind that, then freeze the casserole in a glass container for up to 3 months. Make sure to let the casserole completely cool before placing it in the freezer.

To reheat, defrost in the fridge overnight. Then, place the casserole in the oven until it’s completely warmed through.

white plate with italian spaghetti squash and gold fork and casserole dish behind the plate


If you’re craving Italian food, you should try this Whole30 Italian Stuffed Peppers (Paleo, Keto, dairy free, and gluten free too) and these Italian Chicken Meatballs (Paleo, Whole30 & Keto).

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Baked Italian Spaghetti Squash Casserole (Paleo, Whole30, Keto)

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5 from 1 review


This Paleo & Whole30 Spaghetti Squash Casserole is the perfect weeknight dish that the whole family will love! It’s a healthier, low carb version of your favorite Italian-spaghetti dish. You won’t miss the noodles! Paleo, Whole30, and Keto too!



For the squash:

  • 1 medium-large spaghetti squash
  • 2 teaspoons extra-virgin olive oil
  • 1 teaspoon sea salt
  • 1/2 teaspoon black pepper

For the meat sauce:


  1. Preheat the oven to 400 degrees Fahrenheit. To soften the spaghetti squash before cooking, poke holes in the squash with a fork, and place the whole spaghetti squash in the microwave. Heat for 3-4 minutes. Take spaghetti squash out of the microwave with oven mitts, as the squash will be hot. Trim the ends of the squash, and slice evenly in half.
  2. Scoop out the seeds and stringy parts in the center of the squash. Spray or drizzle the inside of the squash with olive oil, and sprinkle with sea salt. Place squash halves cut side down and bake for 30-35 minutes, or until squash is tender when poked with a fork. Smaller squash will need less time, than larger squash.
  3. While squash is cooking, heat oil in a skillet over medium heat. Add garlic and onion and saute for 2-3 minutes or until onion becomes soft. Brown ground beef, breaking up chunks, until no longer pink. Add Italian seasoning, basil, garlic powder, sea salt, tomato paste, tomato sauce, and diced tomatoes to skillet. Simmer mixture in skillet for 5 minutes.
  4. When squash is finished cooking, flip the spaghetti squash over, and run a fork down the sides and middle of the squash, scraping the squash out of the boat. Add the squash to a large bowl. In the same bowl, add beef skillet mixture. Stir squash and beef mixture together until all squash is covered. Add the eggs, and stir again.
  5. Preheat oven to 400 degrees. Grease a 9×13 baking dish. Pour squash mixture into casserole dish. Bake for 25 minutes. Serve immediately.


To make Vegan: omit the ground beef

  • Prep Time: 5 minutes
  • Cook Time: 55 minutes
  • Category: Main Dish
  • Method: Oven
  • Cuisine: American


  • Serving Size:
  • Calories: 233
  • Sugar: 4.7 g
  • Sodium: 64.4 mg
  • Fat: 15.6 g
  • Carbohydrates: 8.3 g
  • Protein: 15.5 g
  • Cholesterol: 51.4 mg

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    1. Yes it does reheat well. Reheat over low heat in a skillet on the stovetop, in the oven at 350 F, or in the microwave. Oven and stovetop will give you the best consistency.

  1. It was sooo good!!!! I made some modifications by substituting ground beef for ground turkey, chopped up some additional veggies (yellow squash and broccoli) and added some fennel seed for a bit of sweetness!!! The entire family loved it and I have some real picky eaters 🙂

    1. Hello, my website was not working at the time, but it is all available now. I apologize for the inconvenience.

  2. I may have overlooked it, but I don’t see number of eggs to use in the recipe..just add the beaten eggs. I thought I read two, but now can’t find anything. Please help!

  3. Hey just a quick question! In step 4 of the recipe it says add the eggs? I don’t see eggs in the ingredient list??? So I was just wondering how many??
    Thank you 🙂