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Is Chocolate AIP (Autoimmune-Friendly)?

Louise | September 27
Is Chocolate AIP?


It’s the Achilles’ heel in my diet. While I’ve never been a big fan of milk or white chocolate, dark chocolate has been my trusted companion since I can remember.

Luckily, dark chocolate is OK on a Paleo diet in moderation, but what about on the Paleo autoimmune protocol (AIP)?

Is Chocolate AIP (Autoimmune-Friendly)?

Short Answer: Probably Not

I’m sorry to disappoint you, but chocolate is generally not considered autoimmune-friendly.

You’re probably thinking there’s some loophole because I used the words “probably not” and “generally,” but I don’t want to get your hopes up. It’s really best if you don’t eat chocolate on the AIP diet.

So what do the experts say?

Angie Alt, a Certified Health Coach and Nutritional Therapy Consultant, says that chocolate – and coffee – are “misleadingly referred to as beans, but they are actually seeds. Seeds contain protective compounds that can be awfully tough on our systems.”  She’s referring to the phytic acid, or phytates that are high in cocoa products (more on this in a bit).

Paleo Mom, Sarah Ballantyne, PhD, agrees: “Along with blocking mineral absorption, phytates also limit the activity of a variety of digestive enzymes.”  This can lead to increased gut permeability (“leaky gut”) and bacterial overgrowth.

Perhaps this is why seeds, along with nuts, are common food intolerances among those with autoimmune illness (e.g., Crohn’s disease). (1)

So, what’s the loophole then?

There’s no specific link between chocolate and autoimmune conditions or leaky gut. And less-strict versions of the Paleo autoimmune protocol (like the one in Robb Wolf’s book, The Paleo Solution) don’t mention anything about chocolate.

So, should you eat chocolate on the Paleo autoimmune protocol (AIP)?

As with anything in life, the choice is yours. My thoughts would be to eliminate it initially and then to introduce it and see whether it affects your autoimmune condition or not.

Scientific Reasons Why Chocolate Isn’t Allowed on AIP

If you’re like me, then you might want to delve beneath the surface and understand why something is the case. So, when someone tells me that chocolate isn’t autoimmune-friendly, I want to know why!

So, what’s unhealthy about chocolate?

1. Added sugar and non-Paleo ingredients

First, there’s the obvious: most chocolate is made into processed desserts that contain a bunch of unhealthy ingredients like sugar, milk solids, soy, etc.

But what about pure dark chocolate? Ok, read on!

2. Phytic acid

Phytic acid is a substance naturally present in chocolate as well as various other plant-derived foods like nuts, seeds, beans, and grains. Phytic acid can prevent us from absorbing many of the nutrients in the meal we’re eating. (2)

For that reason, it’s often called an anti-nutrient. So, eating chocolate as a dessert can mean that you don’t absorb as many of the minerals from the rest of the food you ate that meal.

This is problematic in those with autoimmune conditions as they often already have impaired digestive issues and mineral deficiencies. If a food item might interfere with absorbing the nutrients in the meal, it should be avoided.

3. Caffeine

It does contain several different chemicals that act as stimulants. There’s a small amount of caffeine in chocolate (generally less than a cup of tea) and also another mild stimulant called theobromine. (3)

One oz of dark chocolate contains around 23 mg of caffeine. (4) For the sake of comparison, a cup of coffee has around 100 mg of caffeine. (5

So, what’s wrong with caffeine?

Caffeine has been linked to rises in cortisol levels and increased inflammation. (6, 7) While there’s no definitive science suggesting caffeine is good or bad for our general health, Sarah Ballantyne suggests limiting caffeine intake for those on AIP

She says, “It’s likely that coffee is helpful for some people with autoimmune disease, but drives autoimmune disease activity in others, therefore the best practice is to eliminate coffee initially on the Autoimmune Protocol and reintroduce later.”

What’s wrong with theobromine?

Generally nothing seems to be wrong with it – it seems to be safe for humans (though very toxic for animals). In fact, some people think theobromine is a better version of caffeine. (8)

Some recent studies actually show cognitive and heart-health benefits associated with consuming theobromine. (9, 10)

4. Toxic metals

Chocolate can actually contain toxic ingredients you won’t find on the label.  Studies have found unacceptably high levels of nickel, cadmium and lead, all poisonous heavy metals, in chocolate produced by multiple manufacturers. (11, 12)

When your immune system is already overburdened, the last thing you need are heavy metals in your food! 

A Few Less Scientific Reasons To Not Eat Chocolate On AIP

It’s easy to overeat

I probably don’t need to show you any science for this one – I’m sure you’ve experienced it yourself!

Chocolate just makes me feel bad

Ok, it doesn’t make me personally feel bad, but I have heard anecdotal stories about people feeling worse if they eat even dark chocolate. Jeremy is one of these people, as is Sarah Ballantyne.

Most brands contains soy lecithin

If you look carefully at the ingredients list of most chocolate bars, you’ll find soy lecithin listed at the end. Soy lecithin is an emulsifier that is used to produce a smoother texture.

While soy lecithin is not particularly healthy, it’s also not the worst thing you can eat. You can find a fair number of brands that do not have soy lecithin as an ingredient if you want to avoid it.


So, as you can see, dark chocolate isn’t all that bad, and it definitely has a fair amount of beneficial properties (like antioxidants and minerals). However, since some people do feel better without it, it’s worth eliminating from your diet – at least temporarily.

Substitutes for Chocolate on AIP

What can you eat instead when you’re on the Paleo autoimmune protocol and craving for a bar of delicious chocolate?

Carob is a great substitute.

carob powder

Carob doesn’t contain caffeine and has a fair amount of vitamins and minerals. However, when you buy carob, make sure to buy pure carob powder (check the ingredients list to make sure carob is the only ingredient). Carob chips will contain non- Paleo and non-AIP ingredients, unfortunately.

This carob powder is 100% pure carob.

Then use the carob powder to make your own AIP “chocolate” treats, like some of the recipes listed below.

AIP “Chocolate” Dessert Recipes with Carob

1. “Chocolate” Carob Fudge

2. “Chocolate” Carob Bread with Date Caramel Spread

3. Brownies

4. Raspberry Carob Truffles

5. Avocado Carob Fudge Bars

6. Carob Snacking Cake

7. Carob Fudge Popsicles

8. Carob Coconut No-Bake Cookies

9. Carob Chip Bars

10. Raw Coconut Macaroons with “Chocolate” Ganache

11. Carob Pumpkin Tart

12. Pomegranate Carob Bark

13. Orange Chocolate Cake

When you reintroduce chocolate into your diet…

Quality is everything.

Most chocolate is filled with non-Paleo (and obviously non-AIP) ingredients. For example, milk chocolate contains a ton of sugar and dairy products. So, you should avoid those regardless.

Same goes for white chocolate – there’s usually a milk product as well as lots of sugar in it.  Better to pick a dark chocolate (over 85% if possible).

Lastly, try to find a brand that tests low for toxic heavy metals. Here’s a great resource

Images: Copyright (c) photka, ayusloth from Fotolia

Beth Massingham

After following a paleo diet for 10 months I’ve found that chocolate is the main cause of my dry eye condition. Still need to have the occasional choccy fix though!


Not sure, why you discuss chocolate and AIP when you list recipes with salt, which is not even paleo to be honest?

    Jeremy Hendon


    Salt is a question a lot of people still have. But salt is entirely Paleo from every possible perspective. It’s been eaten by humans (and every other animal) for the entirety of history.

    More importantly, salt is generally non-inflammatory, and it’s nutritious in the respect that humans need adequate sodium for a variety of physiological purposes. One issue I often see among people transitioning from a SAD to Paleo diet is that they actually eat too little sodium, because processed food generally contains plenty, but it needs to be added to whole foods. This is a particular problem for active people and athletes who sweat out a lot of sodium or for anyone who drinks a lot of water.

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