Low-FODMAP and Paleo Autoimmune Protocol

UPDATE: This post remains one of the most consistently visited on my blog, even five years after I originally wrote it. That tells me that there remains a huge need for information and recipes that help people follow the Paleo autoimmune protocol (AIP) while also managing digestive issues and navigating FODMAP restrictions. I’ve learned a lot in the years since, both through my own personal experience and in my work as a Nutritional Therapy Practitioner. What I wrote in 2013 is still accurate and may be helpful to some, but I want to add an important point now in 2018:

Do not fall into the trap of restricting more and more foods in search of healing. You should not need to avoid high FODMAP foods forever. If you find that you can not reintroduce them in at least moderate quantities, I strongly recommend you seek the assistance of a medical care provider to help you do some troubleshooting.

We spent a glorious day last weekend picking apples. I ate my share in the orchard, sampling as I picked to make sure I liked each variety. Then we came home and I made applesauce, sampling some more. Then I made a grain free apple tart for company we had coming the next day and sampled that too.

And then I paid for it. Truth be told, my stomach was hurting already after just a couple big samples at the orchard but the apples were just so alluring that I failed to listen to the signals that I was overdoing it. I ended up with cramps, gas, and a few extra visits to the restroom. One day wouldn’t have been too bad, but then it stretched into the next day, and then the third day. Only now, on day four, do I feel myself coming back to the happy baseline I had achieved through strict adherence to the paleo autoimmune protocol.

But apples are paleo, right? And they aren’t nightshades or nuts or seeds, or anything else generally restricted on the autoimmune protocol. So what gives?

The answer: Apples contain high amounts of fructose and polyols, both of which are FODMAPs.

What is a FODMAP?

If you have Crohn’s disease, ulcerative colitis, irritable bowel syndrome (IBS) or another digestive disorder or issue, you may have heard the acronym FODMAP which refers to certain foods that can cause and exacerbate bowel symptoms in people who are sensitive to them. A low-FODMAP diet eliminates or minimizes these foods and can be particularly effective to promote healing and minimize symptoms while the autoimmune component of the disease is being brought under control by following a paleo autoimmune protocol (AIP).

This strange term stands for this tongue twister: Fermentable Oligosaccharides, Disaccharides, Monosaccharides and Polyols (you can see why they came up with an acronym!). These are carbohydrates that are not absorbed in the small intestine and may pass into the large intestine where bacteria ferment them, resulting in bloating and gas. This occurs in many individuals and does not cause significant issues for them, but for others it results in symptoms of IBS including abdominal pain, nausea, diarrhea and/or constipation, flatulence and other gastrointestinal symptoms. It is not exactly clear why FODMAPs bother some people with the inflammatory bowel diseases (IBD), but pilot studies have shown that following a low-FODMAP diet does help reduce symptoms in people with active Crohn’s disease.

What is a low-FODMAP diet?

The low-FODMAP diet was developed at Monash University in Melbourne, Australia in the late 1990s and early 2000s. Many of the foods that contain high levels of FODMAPs are otherwise quite healthy and would ordinarily be a staple part of a paleo diet. The good news is that FODMAP sensitivity is dose dependent so most people are able to eat FODMAP foods as long as they keep the amount in check and many people are able to eat some or all of the FODMAP foods when their disease is not active, returning only to FODMAP elimination when and if symptoms begin to return.

Personally, since going paleo and getting my disease mostly under control, I can eat high FODMAP foods as long as I don’t over-do them and am otherwise feeling good. If I do overdo it with one FODMAP food (like the apples) then I start to become sensitive to others that I normally tolerate just fine (like onions and sweet potatoes). To reset my system and get back to feeling good I have to cut back on all the FODMAP foods for a couple days.

So what can I eat if I’m on AIP and eating low-FODMAP?

Being on both a low-FODMAP and paleo autoimmune protocol diet can seem extremely limiting. A wide range of foods contain high levels of the various FODMAPS and unfortunately, not every source agrees on exactly what they are. A nice starting point is the Monash University list (they also have an iPhone app with even more detail). The list can be overwhelming, especially when you are also eliminating so many other foods.

Instead of looking at the off-limits foods, I like to list out what I can eat. Here are my personal guiding principles when I need to simplify my diet and get things back under control:

1. Continue the AIP protocol.

Continue eating a clean paleo diet and continue avoiding foods that are autoimmune triggers for you. This may include all nightshades (tomatoes, potatoes, eggplant, and peppers), dairy, nuts, seeds, eggs, chocolate, and alcohol. If you have successfully reintroduced any AIP foods, you may choose to avoid them while you are letting your digestive system reset, or you might decide to continue eating them. So far I have reintroduced eggs, potatoes, and small amounts of dark chocolate and I decided to keep eating them after my recent overindulgence in apples, but perhaps I would have bounced back to normal more quickly if I did eliminate them. I don’t plan on there being a next time, but if there is I will probably try cutting those foods back out also.

2. Embrace your inner carnivore.

All meat is allowed, both on AIP and the low-FODMAP diet. Plus, when the body has been stressed and is reacting negatively, it needs the nourishing proteins and fats more than ever. To get myself back to normal I load up on well cooked, easy to digest meat and drink lots of bone broth throughout the day.

3. Eat plenty of safe vegetables.

These AIP-friendly vegetables are all low-FODMAP and  should be fine in any quantity:

  • carrots
  • cucumbers
  • kale
  • lettuce
  • okra
  • parsnips
  • pumpkin
  • radishes
  • spinach
  • zucchini and other summer squash

As long as you keep the serving to a moderate size, these additional vegetables should be well tolerated by most:

  • broccoli
  • Brussels sprouts
  • cabbage
  • fennel
  • sweet potatoes and yams
  • turnips
  • winter squash, all types

Keep in mind that you may find that you tolerate some vegetables better than others and that cooked vegetables work better for you than raw. Your personal “safe” list might be shorter than this one

4. Let fruit be your treats, but keep it to a minimum.

Be mindful of your own personal tolerance level for fruits. In larger quantities, even the low-FODMAP fruits can end up providing a dose of fructose that is bigger than many people can handle and also contributes to inflammation. Also, many people with autoimmune diseases are very sensitive to blood sugar changes and need to limit their consumption to eating fruit only with meals in order to avoid spikes.

In terms of FODMAP content, these are fruits that all should be able to tolerate:

  • bananas
  • blueberries
  • cantaloupe
  • grapes
  • honeydew melons
  • kiwi
  • oranges and other citrus fruits
  • pineapple
  • raspberries
  • rhubarb

4. Give coconut products a try

Early FODMAP testing showed that coconut was high in sorbitol but more recent testing has shown this not to the case and Monash University now lists it as low-FODMAP. However, some people do not tolerate it well regardless so be cautious. Personally, I have found that coconut products of all types work very well with my body, even when my digestion is iffy, so I load up on it as a good source of healthy fats.

Low-FODMAP and AIP recipes from Gutsy By Nature

(Check the notes for each, some may require slight modifications to be both AIP and low-FODMAP)

Main Dishes
Side Dishes

Other great resources

My friend Christina of A Clean Plate has a great e-book called 28 Days of Low-FODMAP AIP that is a great jump start for anyone beginning AIP and also eliminating high FODMAP foods. It includes recipes as well as meal plans and shopping lists and is bargain priced at just $9.99!


Also, the recipes in these cookbooks indicate FODMAP status and provide modifications whenever possible. I cook from all frequently and highly recommend them!


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Low-FODMAP and Paleo Autoimmune Protocol - Gutsy By Nature

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