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 βpastaβ 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 youβll 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 youβll 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 arenβt a fan of spaghetti squash or donβt 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 β Iβve 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 Iβm 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! Iβm sure it would be good like that tooβ¦ π

Paleo Spaghetti Recipe (AIP & Low FODMAP)
Ingredients
- 3 spaghetti squash
- 2 796 ml canned pumpkin
- 2 lb ground beef
- 1 lb mushrooms (Omit or greatly reduce for low FODMAP)
- 1 cup bone broth (250 ml)
- 1 cup fresh basil
- 1 tbsp dried oregano
- 1 tbsp dried parsley
- 1 tsp dried rosemary
- 1 tsp dried thyme
- 1/2 tsp sage
- 1 tbsp salt
Instructions
- Preheat your oven to 350 F
- Cut your spaghetti squashes in half lengthwise
- Using a spoon or squash scraper, scoop out all the seeds
- 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
- 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
- Dice up your fresh basil and set aside
- On low to medium heat, brown your ground beef
- Add the sliced mushrooms and continue cooking and stirring until it looks cooked through
- Add all dry seasonings & fresh basil and mix everything together. Leave out a small amount of fresh basil for garnish at the end.
- Add canned pumpkin and bone broth and mix well
- 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
- 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
- Top spaghetti squash with sauce and serve
Video
Nutrition
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Looking for more AIP or low FODMAP recipes?
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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.
Why do you say it’s low FODMAP but use 1 lb of mushrooms? Everything I’ve researched says mushrooms are high in mannitol even in small amounts.
Hey there, I appreciate you pointing that out. I thought I had a note on the recipe card to omit or greatly reduce the mushrooms for low FODMAP, but I didn’t! I have added it now. Thank you so much. π