This paleo spaghetti recipe is fully compliant with the autoimmune paleo protocol (AIP) and is also Low FODMAP for people with sensitive digestion or IBS. This recipe uses spaghetti squash as the “pasta” base and an aip spaghetti sauce on top, with a pinch of fresh basil for garnish and extra flavour. The spaghetti 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. 

This recipe is great if you want to balance your hormones, stabilize your blood sugar, ease IBS symptoms, or lower inflammation in your body.

What you’ll need for this recipe

The equipment you will need for this recipe is:

  • cutting board
  • 2 baking sheets
  • parchment paper
  • large sharp kitchen knife
  • oven
  • large pot
  • squash scraper tool (Optional: for scraping out seeds from the spaghetti squash. You can also use a spoon.)

How to make this paleo spaghetti recipe

The full instructions for this recipe can be found below in the recipe card, but you can also watch it being made step-by-step by checking out the video below.

Recipe substitutions or variations 

Pasta base: If you aren’t a fan of spaghetti squash or don’t have access to any, you can also use the following pastas and pasta substitutes as the base:

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

Spaghetti sauce: This AIP spaghetti sauce is made with canned pumpkin, but can also be made with regular tomato sauce/canned tomato 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!

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

Recipe pairing ideas 

This paleo spaghetti recipe can be served with AIP biscuits as a side (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 divy 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 at least six servings in every batch of this paleo spaghetti recipe. And it freezes well.

Can I use this recipe for just the AIP spaghetti sauce?

Yes, if you just want the sauce recipe, simply leave out 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 hell, just eat it straight! I’m sure it would be good like that too… 😆

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 from 2 votes
Prep Time 15 mins
Cook Time 1 hr
Total Time 1 hr 15 mins
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 its reached the desired consistency you want
  • 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 looks 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 burner down to low 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 each 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 spaghetti squash with sauce and serve
    picture of aip spaghetti sauce on top of baked spaghetti squash



Calories: 432kcalCarbohydrates: 40.8gProtein: 38.7gFat: 15.6gSaturated Fat: 6.8gPolyunsaturated Fat: 0.6gMonounsaturated Fat: 0.2gCholesterol: 93.3mgSodium: 1329mgPotassium: 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.