The paleo autoimmune protocol cuts out nightshades, nuts, seeds and eggs.
Coconut is technically a nut so is it allowed?
What about cocoa which is technically a bean?
Coconut is not a true nut so it should be fine unless one has an allergy to it.
Cocoa is a no, sorry to say. Also I would add dairy and NSAIDs to your autoimmune protocol avoid list as they also can be gut irritants.
It has been hard for me to avoid chocolate, but I have come to realize that it really makes me feel awful after I eat it and makes sense that it is not included in the protocol.
When my functional medicine doc put me on an autoimmune protocol, she promoted coconut and I did well on it.
Not sure how cocoa could be a problem, I wouldn't worry about a little here and there. Or, if you are super stoked on health goals, omit anything you aren't sure about then you know for sure it's not holding you back. Introduce it again in a month or so and see how you feel.
Chocolate and cocoa come from cacao, the seed of a fruit. It is only called a bean because of it's appearance. It is not a legume. Seeds are part of the Paleo diet but are restricted on the AutoImmune Protocol until the gut is healed. Then you can try reintroducing it. I think the main concerns with chocolate stem from the high sugar content in many chocolate treats, and that it is high in phytic acid - See the PaleoMom's post on chocolate here
Also, it isn't really a paleolithic food as cultivation began only in 1500 BC-400 BC. See more about the history here.