AIP Butternut Squash Soup with Bone Broth and Coconut Milk

This butternut squash soup is built on homemade bone broth and coconut milk, with coconut aminos, fish sauce, ginger and garlic for a savory base. The squash and any root vegetables you add roast first at 400°F (204°C) until browned, then simmer in the broth and get blended smooth. Every ingredient is on the AIP elimination-phase list, and the soup is dairy free, nightshade free and seed free. It also fits paleo and Whole30 as written. It is a warming dinner for the cold months and pairs well with beef or chicken.

Key takeaways

• Roast the squash cut side down at 400°F (204°C) for 30 to 45 minutes depending on its size, then scoop the flesh out of the skin.
• Homemade bone broth is the base, but vegetable stock or any compliant broth you have on hand works.
• Use a canned coconut milk whose only ingredient is coconut, with no gums or thickeners.
• Blend with a stick blender, then thin with more broth or coconut milk to the texture you like.
• Serve with beef or chicken for a full meal.

This article is for education only and does not diagnose, treat or replace care from a qualified practitioner. I am a clinical herbalist, not a physician. The Autoimmune Protocol is an elimination diet, and anyone managing an autoimmune condition should talk with their own provider before making large changes to how they eat. Do not start, stop or change any medication based on this article. People respond to foods differently.

What makes a soup AIP compliant

Evidence: limited. A few small, uncontrolled human trials, with no randomized trials published so far.

The Autoimmune Protocol (AIP) is a stricter elimination diet built on paleo eating. During the elimination phase it removes grains, legumes, dairy, eggs, nuts, seeds, nightshades, refined sugar, seed oils and alcohol, then reintroduces foods one at a time to see which ones a person tolerates. For a soup, that rules out cream, butter, white potato, black pepper, seed-based spices such as cumin and coriander, and most store-bought broths and stocks, which often contain tomato, pepper or undisclosed "spices." My AIP diet guide covers the full food list and the reintroduction stages.

The research on AIP is small. A 2017 trial at Scripps Clinic followed 15 adults with active Crohn's disease or ulcerative colitis through a 6-week elimination phase and a 5-week maintenance phase, and the researchers recorded improvements in symptom scores by week 6.^[1] A follow-up paper on the same group reported quality-of-life scores improving as early as week 3.^[2] A 2019 pilot study of 16 women with Hashimoto's thyroiditis on a 10-week AIP coaching program recorded lower symptom scores and lower hs-CRP, but no significant changes in thyroid hormone levels or thyroid antibodies.^[3] None of these studies had a control group, and the authors of each called for larger randomized trials.

Ingredients

Serves 4.

• 1 medium butternut squash
• 1 tablespoon coconut oil, for the pan
• Optional root vegetables for the roasting pan: half an onion, 2 carrots, 1 parsnip, 1 sweet potato
• 2 to 3 cups bone broth, vegetable stock or any compliant broth you have on hand
• 1 can (13.5 oz / 400 ml) coconut milk, with coconut as the only ingredient
• 2 tablespoons coconut aminos
• 2 teaspoons fish sauce (I use Red Boat, which is anchovies and salt only)
• 1 thumb-sized piece of fresh ginger, grated
• 3 cloves garlic, crushed and then chopped fine
• 1 tablespoon flaky sea salt (I use Maldon), plus more to taste. If you use fine sea salt, start with half that amount.
• Fresh parsley, to garnish

How to make AIP butternut squash soup

Roast the squash

1. Heat the oven to 400°F (204°C).
2. Cut the squash in half lengthwise and scoop out the seeds. Rub the cut sides with coconut oil so they do not stick, and set the halves cut side down on a sheet pan.
3. If you are adding root vegetables, put them on the same pan. Onion, carrots, parsnips and sweet potato can roast whole or in large pieces with the skin on. Coat them in a little coconut oil as well.
4. Roast for 30 to 45 minutes depending on the size of the squash, until everything is lightly browned and a knife slides through the squash with no resistance.
5. Let everything cool on the pan until you can handle it.

Simmer and blend

6. Scoop the squash flesh out of the skin and put it in a stock pot. Slip the skins off the sweet potato and any other vegetable that has one, and add the vegetables to the pot.
7. Add 2 to 3 cups of broth, the can of coconut milk, coconut aminos, fish sauce, grated ginger, garlic and salt.
8. Bring to a simmer and cook for about 20 minutes, until the squash and any other vegetables mash with no effort against the side of the pot.
9. Blend with a stick blender until smooth. Add more broth or coconut milk here to adjust the thickness. I like it thick enough to coat a spoon, but you can thin it to something you could drink from a mug.
10. Taste and adjust the salt before serving. Ladle into bowls and top each with a sprig of parsley.

Handmade in Montana

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Why every ingredient is AIP compliant

Evidence: based on the standard AIP elimination-phase food list.

Bone broth, vegetable stock or other broth

Homemade bone broth is compliant as long as it was made without black pepper or nightshades. My chicken bone broth includes black pepper, so leave it out of the pot if you are making a batch for this soup. The collagen and gelatin that cook out of the bones are covered in my article on foods high in collagen. If you use a store-bought broth or vegetable stock, read the label. Many contain tomato, pepper, celery seed, "spices" or "natural flavors," and any of those puts it off the list.

Coconut milk

Coconut is allowed on AIP, but most canned coconut milk contains guar gum or other thickeners, which many AIP guides treat as a gray area. Pick a can whose ingredient list says coconut milk and nothing else. Some brands list coconut and water, which is fine. Shake the can well or stir the thick cream back in before pouring.

Coconut aminos and fish sauce

Coconut aminos are the AIP stand-in for soy sauce and are made from coconut sap and salt. Fish sauce is compliant when the only ingredients are fish and salt, which is the case for Red Boat. Some brands add sugar, MSG or hydrolyzed wheat protein, and those are not compliant.

Ginger, garlic, onion and parsley

Ginger is a root spice, and AIP only removes the seed-based spices. Garlic and onion are alliums, which are allowed, and parsley is a leaf herb. Black pepper is left out of this recipe because most AIP food lists put it in the first group of foods to reintroduce rather than in the elimination phase.

Squash, root vegetables, coconut oil and salt

Butternut squash, carrots, parsnips and sweet potato are all on the elimination list. White potato is the one root vegetable AIP removes, because it is a nightshade, so do not add it to the roasting pan. Coconut oil is on the AIP fats list, and any unrefined sea salt works.

Serving and swaps

The soup is filling on its own, but it pairs well with beef or chicken as a full dinner. Shredded meat from an Instant Pot whole chicken can go straight into the bowl, or serve the soup next to a plate of AIP sheet pan root vegetables and roast beef.

• Other squash: kabocha, acorn or a small pie pumpkin roast the same way and can replace the butternut.
• More roots: turnip, rutabaga or celery root can go on the roasting pan. Each one makes the soup a little less sweet.
• Thicker soup: add a second sweet potato to the roast. It thickens the blend without changing the flavor much.
• No fish sauce: add another tablespoon of coconut aminos and a pinch more salt.
• Richer finish: stir a spoonful of coconut cream into each bowl before the parsley goes on.

Storage and reheating

The soup keeps 4 days in the fridge in a sealed container. It thickens as it cools, so reheat it on the stove over low heat with a splash of broth or water and stir until smooth. It also freezes well for up to 3 months. Freeze it in wide-mouth jars with 1 inch of headspace, thaw overnight in the fridge, and reheat the same way.

Frequently asked questions

Is butternut squash allowed on AIP?

Yes. The flesh of all winter squash is on the elimination-phase list. The seeds are not, since AIP removes all seeds, so scoop them out before roasting.

Is this soup paleo and Whole30 compliant?

Yes, as written. Paleo removes grains, legumes, dairy and refined sugar, and Whole30 also removes added sugar, alcohol and additives such as carrageenan, MSG and sulfites. None of the ingredients here contain any of those. Coconut aminos and fish sauce made from fish and salt only are both on the Whole30 allowed list.

Can I use vegetable stock instead of bone broth?

Yes. Any broth or stock works as the base as long as the ingredients are compliant. Check store-bought stock for tomato, pepper, celery seed, "spices" or "natural flavors."

Why does the coconut milk need to be gum free?

Guar gum and other thickeners are treated as a gray area on most AIP food lists. A can that lists only coconut milk keeps the recipe inside the elimination phase.

Can I make this without roasting the squash?

You can peel and cube the squash and simmer it in the broth until soft, which takes about 25 minutes. Roasting first browns the squash and gives the soup a deeper flavor, so I roast it when I have the time.

Can I blend this in a regular blender instead of a stick blender?

Yes. Let the soup cool for 10 minutes first, fill the blender no more than halfway, and leave the lid vent open with a towel over it so steam can escape. Blend in batches and return everything to the pot.

Sources

1. Konijeti GG, Kim N, Lewis JD, et al. Efficacy of the Autoimmune Protocol Diet for Inflammatory Bowel Disease. Inflamm Bowel Dis. 2017;23(11):2054-2060. doi:10.1097/MIB.0000000000001221. PMID: 28858071. Uncontrolled trial with 15 participants. The PubMed record lists NIH and non-government research support.
2. Chandrasekaran A, Groven S, Lewis JD, et al. An Autoimmune Protocol Diet Improves Patient-Reported Quality of Life in Inflammatory Bowel Disease. Crohns Colitis 360. 2019;1(3):otz019. doi:10.1093/crocol/otz019. PMID: 31832627. Same 15-person cohort as source 1, with no control group.
3. Abbott RD, Sadowski A, Alt AG. Efficacy of the Autoimmune Protocol Diet as Part of a Multi-disciplinary, Supported Lifestyle Intervention for Hashimoto's Thyroiditis. Cureus. 2019;11(4):e4556. doi:10.7759/cureus.4556. PMID: 31275780. Uncontrolled pilot study with 16 participants who completed it. Two authors are listed as independent researchers in private practice, and co-author Angela Alt helped develop the AIP coaching program that was tested.