This paleo spaghetti is fully compliant with the paleo diet, autoimmune protocol (AIP diet), and Low-FODMAP diet. It uses spaghetti squash as the “pasta” base and a spaghetti sauce on top, with a pinch of fresh basil for garnish and extra flavor. The sauce is made from canned pumpkin instead of tomatoes, which may sound strange at first but you’ll be surprised to see that pumpkin has a very similar profile to tomatoes, with a similar texture and level of acidity. 

Below you’ll find the recipe instructions along with details about substitutions and variations that can be made to suit any meal plans you might be following.

Recipe ingredient substitutions  

Pasta base: If you aren’t a fan of spaghetti squash or don’t have access to any, you can use the following pastas and pasta substitutes as the base. Keep in mind, not all of these are AIP and low FODMAP.

  • zucchini noodles
  • butternut squash noodles
  • sweet potato noodles 
  • shirataki noodles
  • gluten-free spaghetti noodles
  • Almond flour noodles

This is essentially a meat sauce recipe so all of these will work as a noodle base.

Spaghetti sauce: This spaghetti sauce is made with canned pumpkin, but can also be made with regular tomato sauce, canned tomato, and/or tomato paste if you are not intolerant to tomatoes. Or you can also do half pumpkin and half tomato – I’ve tried this and it also tastes great! Keep in mind, tomatoes are low FODMAP but not AIP.

Add onion and garlic: Because this recipe is also low FODMAP, I have not included onion or garlic in the sauce. If you tolerate fresh garlic and onions, feel free to add them. Start with one chopped onion and 2 to 3 garlic cloves, or half a teaspoon of each onion powder and garlic powder if you are doing dried.

Seasonings: For this recipe I use the classic Italian seasonings. You can also add chili flakes, paprika, bay leaf, nutritional yeast, coconut aminos, or other fresh herbs. Be careful though, some of these seasonings are not AIP or low fodmap diet compliant. 

Recipe variations

Make this recipe higher protein: Instead of ground beef, use ground chicken. You’ll need to use a bit of olive oil or coconut oil to prevent the chicken from sticking while cooking.

Make this recipe lower carb: Use a low carb noodle like zucchini noodles or shirataki. You can also use a higher fat red meat like ground pork for keto.

Make this recipe creamier: If you want more of a creamy sauce consistency, add some canned coconut milk.

Add extra vegetables: If you want to bring up the vegetable content, you can add things like carrots, celery, sweet potatoes, and red bell pepper to your sauce.  Not all of these ingredients are AIP or low FODMAP though.

Recipe pairing ideas 

This spaghetti can be served with AIP biscuits as a side dish – check out this great recipe by Eat Beautiful

Or these AIP breadsticks recipe by Primal Palate!

Recipe frequently asked questions

Does paleo spaghetti freeze well?

Yes! I often make this recipe when I am doing weekly meal prep, and then I divvy everything out into six servings in glass containers and freeze until I’m ready to eat it.

Can I use this recipe for meal prep?

Yes, this recipe is actually perfect for meal prep because you get a big batch with at least six servings of this paleo spaghetti sauce. It freezes well.

Can I use this recipe for just the spaghetti sauce?

Yes, if you just want the sauce recipe, simply leave out the spaghetti squashes and the instructions that relate to baking those. The sauce is quick and easy to make on its own, and you can prepare it with any of the pasta substitutions I mentioned above in this post. Or heck, just eat it straight! I’m sure it would be good like that too… 😆

Can I make this recipe in a slow cooker?

Yes!  Throw everything in and cook on low for 8 hours. 

My sauce is pretty runny, is there anything I can do to thicken it up?

Yes!  There are lots of reasons why this could have happened. You may have added a bit too much bone broth, or maybe a lot of liquid came out of the mushrooms. Either way, start with a tablespoon of tapioca flour sprinkled on top and then mix it in.  Keep adding it a bit at a time until it thickens up.

You might also like:

If you liked this recipe, check out my other paleo beef recipes:

Looking for more AIP or low FODMAP recipes?

Check out my one-month meal plans and recipe books for each.

picture of paleo spaghetti recipe (AIP & Low FODMAP)

Paleo Spaghetti Recipe (AIP & Low FODMAP)

Tara Klippert
This paleo spaghetti recipe is also AIP, Low FODMAP, gluten free, dairy free and sugar free.
4.34 from 3 votes
Prep Time 15 minutes
Cook Time 1 hour
Total Time 1 hour 15 minutes
Course Main Course
Cuisine American, Italian
Servings 6
Calories 432 kcal



  • Preheat your oven to 350 F.
  • Cut your spaghetti squashes in half lengthwise.
  • Using a spoon or squash scraper, scoop out all the seeds.
    hollowed out spaghetti squash
  • Line 2 baking sheets with parchment paper and pour about 1/2 – 1 cup water into each pan.
  • Place all 6 spaghetti squash halves facing down on the baking sheet, making sure to get some water underneath each.
    spaghetti squash face down in pan ready to bake
  • Bake spaghetti squash in the oven for 30-45 minutes, checking after 30 to see if it's reached the desired consistency you want. If you want the spaghetti squash noodles al dente, bake them for less time.
  • While the spaghetti squash is baking, dice up your mushrooms and set aside.
    sliced mushrooms
  • Dice up your fresh basil and set aside.
    fresh chopped basil
  • On low to medium heat, brown your ground beef.
    picture of browning beef in pot
  • Add the sliced mushrooms and continue cooking and stirring until it's cooked through.
    picture of beef and sliced mushrooms simmering in pot
  • Add all dry seasonings & fresh basil and mix everything together. Leave out a small amount of fresh basil for garnish at the end.
    picture of sauce after adding all seasonings and basil
  • Add canned pumpkin and bone broth and mix well.
    picture of adding bone broth and canned pumpkin to spaghetti sauce
  • Turn the burner down to low heat and simmer for at least 15 minutes (or longer if you like!) until the flavours have mingled and the sauce has cooked down a bit.
    picture of AIP spaghetti sauce simmering
  • After taking your spaghetti squash out of the oven and letting it cool, scrape out the flesh of the squash into a large bowl, or into 6 smaller containers if you are doing meal prep.
    picture of hollowed out spaghetti squash and bowl full of cooked squash
  • Top the spaghetti squash with the meat sauce and serve.
    picture of aip spaghetti sauce on top of baked spaghetti squash
  • Store your leftovers in an airtight container in the fridge for 2 – 3 days, or in the freezer for much longer. If you are making this for meal prep, divide it out into individual containers.



Calories: 432kcalCarbohydrates: 40.8gProtein: 38.7gFat: 15.6gSaturated Fat: 6.8gPolyunsaturated Fat: 0.6gMonounsaturated Fat: 0.2gCholesterol: 93.3mgSodium: 748mgPotassium: 1174.4mgFiber: 12.5gSugar: 15.6g
Keyword AIP, dairy free, gluten free, grain free, Low FODMAP, paleo, soy free, sugar free
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Tara Klippert
About the author Tara Klippert

Tara Klippert is a Registered Health and Nutrition Counselor and holds a diploma in Holistic Nutrition and Health Coaching. She shares her gluten free, dairy free & allergy friendly recipes.