This post will be mostly based on anecdotal evidence , but I believe this information is still useful and there is not much harm in the suggested diets. In the worst case, the diet won’t help with autoimmune symptoms, and you’ll just end up eating more vegetables. I don’t think that’s a terrible outcome.
The most popular diet for autoimmune diseases is the Autoimmune Protocol Diet (AIP). Most popular doesn’t mean it has the most evidence to back it up, but for whatever reason, it got around the internet. The AIP diet excludes many foods that are considered to be inflammatory and claims to reduce levels of thyroid antibodies. I cannot claim that his mechanism is true as there are almost no scientific papers on this, only anecdotal evidence. On the other hand, this diet is not unhealthy, so I doubt someone would be worse off by trying it. Usually bloggers/naturopaths recommending the diet suggest to try it for at least thirty days. Food groups that are excluded are gluten, all grains, pseudo-grains, dairy, legumes, beans, nuts, seeds, nightshades, eggs, vegetable oils, processed foods, and sugar. I might be forgetting something because there are so many items that get excluded, but if you are interested, you can read about the diet below.
What evidence is there? Well when I googled “AIP diet evidence”, I found one paper. You can try the same Google search. This particular study found that following the AIP diet, 6 weeks elimination phase and 5 weeks maintenance phase, improved endoscopic inflammation in patients with IBD (irritable bowel disease). Only 18 patients were enrolled in the study, so that is a very small sample size. Also such a study does not tell us whether it was necessary for all these food groups to be eliminated, maybe the results would be the same if only gluten and processed foods were eliminated. So it is some evidence that the diet helps but it is only one study and it doesn’t tell us about the mechanism of action of this dietary intervention.
Efficacy of the Autoimmune Protocol Diet for Inflammatory Bowel Disease
Personally I did follow the AIP diet for about a year. When I found out in June 2016 that I had high levels of thyroid antibodies, I finally started to have some hope that maybe I have an autoimmune disease that can be treated instead of treatment resistant schizophrenia and psychotic depression. My mom googled a lot at that time, I didn’t have the energy or motivation to do it, and she convinced me to start trying dietary changes. I started by excluding gluten and dairy and later on went on the AIP diet and stayed on it until December 2017. In June 2016 my Anti-Tg antibodies were over 1000, Anti-TPO was 40 something. Comparing to spring/summer 2016, I did improve by fall 2017, and my Anti-Tg antibodies reduced to about 500. Anti-TPO stayed the same. Was this improvement directly related to the AIP diet and was it necessary for me to eliminate all the food groups? I don’t know the answer to that question. I did go to a gastroenterologist who diagnosed me with chronic gastrointestinal inflammation and advised me to go on a low FODMAP diet. AIP diet overlaps with low FODMAP diet, therefore it could be that it was the elimination of high FODMAP foods that helped me.
The low FODMAP diet is based on the idea that certain foods contain compounds that contribute to gastrointestinal disorders such as IBS. FODMAPS are short chain carbohydrates and sugar alcohols, such as fructose, fructans, galacto-oligosaccharides, lactose, and polyols. Research indicates that some people might not be able to digest these compounds well and this could lead to inflammation in the intestines and gas produced by bacteria as they break down undigested carbohydrates.
Below is a list of high and low FODMAP foods (for those that are FODMAP intolerant it is advised to avoid high FODMAP foods, this can be discussed with a gastrointerologist).
Could a bad diet cause brain inflammation and psychotic depression? Could a change in diet reduce symptoms if there is inflammation? I don’t think at this point we have a concrete answer, there have been studies though which indicate that a specific diet could improve your mood and physical health. Autoimmune encephalitis is quite rare and I haven’t seen studies on AE patients and diet changes, but I still encourage you to consider whether you are eating healthy and to consider making changes. In general, from what I’ve read, many doctors consider the Mediterranean Diet. This diet includes whole grains, a lot of vegetables, yogurt , nuts and seeds, and more fish instead of meat (increasing Omega 3 content). There has been a study with positive results, indicating that Mediterranean diet can help patients with depression.
Mediterranean Diet Depression Article
So which diet is best, should you try a specific diet, which one? There is no medical test for this at the moment, only trial and error. As I mentioned, I was on the Autoimmune Protocol Diet for about a year and I did see an improvement in symptoms and reduction in Anti-Tg antibodies . My gastroenterologist also advised me to stick to a low FODMAP diet due to my abdominal issues and I have been following this advice. After I received the IV steroids treatment in December 2017, I relaxed my AIP dietary restrictions and tested several items. I stick to eating gluten-free free and cow dairy free, also I felt that I had skin/abdominal issues become aggravated by potatoes, peanuts, and hot peppers. I avoid processed foods and vegetable oils.
It sounds restrictive but I found this diet to be working for me and I feel that I have enough variety. I eat a lot of goat/sheep/buffalo plain yogurt with nuts and seeds, tea with goat milk, quail eggs, poultry , seafood. In terms of vegetables – zucchini, carrots, squash, plantains, sweet potatoes, kale, spinach, bell peppers, etc. Grains – black rice, quinoa, buckwheat, oatmeal. For bread I eat sourdough version and sometimes I make cassava flour tortillas. I don’t eat beans and legumes much because they are high FODMAP, sometimes I add canned chickpeas or sprouted mung beans. For cooking I use olive, avocado , and coconut oils.
Notes of a Neuropsychiatry Amateur 
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