Supplements and vitamins for autoimmune disease can be an effective tool for managing autoimmune symptoms, calming inflammation, and addressing nutrient deficiencies. After a decade of experimenting with various supplements, here is what what we personally take for our autoimmune conditions and why.
As a follow-up to my post: 11 Things You Need to Know Before Buying Supplements for Autoimmune Disease, I feel it is only appropriate to tell what supplements for autoimmune disease we’ve landed on after years of experimentation and problem-solving for our own autoimmune issues.
Supplements were a crucial part of our path to reversing autoimmune symptoms, and are still part of our daily lives.
While Frank and I (and our wallet) would love a world where we didn’t have to take supplements, it just isn’t the case for us as the benefits we’ve felt and observed from these are too big to ignore.
So in this post, I’ll reveal all of the supplements we take on a consistent basis, how we picked them, what dosage we use, what benefits we feel, and, most importantly, WHY we take them.
We personally feel the approach to using supplements for autoimmune disease requires a basic understanding of why you are taking them in the first place.
It is so easy to get lost in all the recommendations from your doctor, online influencers, friends, family, etc. Then you may find yourself saying “Well, I tried x, y, and z but it didn’t work for me…” because you had no real understanding behind your supplementation in the first place.
How do I know this?
Because it happened to me. And I don’t want it to happen to you.
Consider supplements for autoimmune disease like an investment – you want to research it and know the reason behind investing before you dump your hard-earned money into it.
If you are looking for a place to start that research, I add in many references and links throughout this post. We also have a free Autoimmune Starter Pack filled the same resources we used to find the supplements we needed. Just click the button below and we will send it over to you for free!
So, without further ado…
Our Favorite Supplements and Vitamins for Autoimmune Disease: What We Take & Why
*Please note that I am not a doctor or medical professional. This site is for informational purposes only and does not provide medical advice. All experiences with these supplements are our own, and we make no guarantees that others will have the same experience.
To help explain the whys behind our supplements, I’m breaking them down into the following categories: nutritional, inflammation management/immune modulation, and therapeutic.
Nutritional Supplements and Vitamins for Autoimmune Disease
By “nutritional”, I mean supplements that do at least one of the following:
- Make-up for a common deficiency associated with autoimmune disease
- Fill in nutritional gaps as a result of our more restricted diet for managing autoimmune symptoms
- Make-up for the nutrients that we are personally deficient in or need more of as evident through either bloodwork or genetic testing
Anna’s Nutritional Supplements:
Magnesium is one of the most common deficiencies (even if you don’t have autoimmune disease), and has numerous benefits.
It’s helpful for insomnia, calming anxiety, constipation, muscle relaxation, and reducing inflammation, and is an essential mineral for bone health/formation and vascular function. To learn more about magnesium, here is a helpful article from Dr. Amy Myers.
Magnesium has changed my life and I do not say that lightly. When I don’t take it, I experience debilitating anxiety, bone pain, muscle aches, tremors, and leg cramps (the kind that make you hop out of bed in the middle of the night).
There are many forms of the nutrient, but Magnesium Glycinate seems to be the one that I tolerate best. All others give me very loose stools.
I take 4 capsules a day (2 in the morning and 2 at night) of the Pure Encapsulations brand which comes out to 480 mg daily. I am bummed at how expensive it is, but I’ve tried switching to a cheaper brand and had poor outcomes.
I am happy to see Vitamin D supplementation become more mainstream and recommended by even conventional medical doctors. There are a plethora of benefits for maintaining adequate levels of Vitamin D, especially for autoimmunity.
Vitamin D was one of the first supplements I ever starting taking at the beginning of my autoimmune discovery (roughly 10 years ago) because it is a common nutrient deficiency not only for autoimmunity, but for everyone. I noticed an immediate difference in my mood and bone pain.
Frank also hopped on board and then we learned how important cofactors like Vitamin K2 and Vitamin A are in supporting Vitamin D as they have a synergistic relationship. So, we found a supplement that contained Vitamin K2 and ensure we get enough Vitamin A through diet.
We supplement with higher amounts during the winter time due to our lack of sun exposure in the Midwest. This helps significantly with beating the winter blues.
Related: 10 Tips to Beat the Winter Blues
We may supplement during the summer if needed, but not on a daily basis because we are out in the sun a lot more. Due to the risk of taking too much Vitamin D, we monitor blood levels about every 3-6 months.
If our vitamin D levels get too low, I tend to experience bone and fibromyalgia-type pain, as well as depression. If Frank’s levels get too low, he too experiences the effects on mood muscle/bone type pains.
The brand we use is Thorne Vitamin D/K2 drops and our dosages vary depending on the season ranging anywhere from 2,000 – 10,000 IUs daily.
Two reasons: my diet does not provide enough calcium, and I am usually pregnant or nursing and need to make sure I have enough for me and the baby.
I am very cautious about calcium supplements (here’s why), and finally found one by Dr. Amy Myers that I felt comfortable taking until I just found out (as I was writing this post), that it’s discontinued!
So, I will be switching to 1-2 capsules every 1-2 days of Grassfed Living Bone by Ancestral Supplements.
Supplements I Take When Following a Plant-Based Diet
Over the years, I continue to experiment with various diets to find what my body likes best. But, some of these diets lack in nutrients that I specifically need.
When I follow a plant-based diet high in raw vegetables (see Dr. Brooke Goldner’s Goodbye Lupus diet for more information), I take the following supplements in addition to the Magnesium, Vitamin D/K2, and Calcium listed above.
This is simply because I’ve battled anemia for years and need to take an iron supplement for sufficient iron levels if I am not consuming enough animal protein.
I notice almost immediately when my iron levels get too low, with the first symptoms being heart palpitations and exhaustion. Maintaining my iron levels is crucial to thyroid health, and because I have a history with Hashimoto’s, this is something I monitor closely.
I’ve tried multiple brands and types over the years – some of which constipated me or made me feel ill. I was taking the gluten-free version of Floradix, which is called Floravital, for a long time, but then discovered that I am sensitive to the combination of B vitamins that are added.
I eventually landed on Thorne’s Iron Bisglycinate. I tolerate it okay, and take 1 capsule (25 mg) every 1-2 days.
(I should note that while the Iron Bisglycinate tides me over when following a plant-based diet, I find that my iron levels respond much better if I have a continuous intake of high-iron animal protein like beef liver and other organs.)
Active B12 with L-Methylfolate
I take this because I have the MTHFR mutation (1 mutation each of the C677T and A1298C), and struggle with high homocysteine levels as a result. If you’ve never heard of the MTHFR mutation and its relation to autoimmune disease, I suggest you read this article by Dr. Amy Myers.
This is also what I use as my source of B12 when I am eating a plant-based diet since B12 is only found in animal foods.
If I do not take this supplement, I experience debilitating anxiety and high homocysteine levels in my bloodwork. It also helps out with iron absorption.
However, I’ve noticed that I am sensitive to high levels of B vitamins, even if they are methylated, and cannot take more than 400 mcg of methylated folate per day without feeling ill and getting a headache.
I use the Seeking Health Active B12 with L-Methyfolate lozenges and take half a lozenge daily (400 mcg) in the morning, dissolved under the tongue.
(For more information on how to treat and test for the MTHFR mutation, I suggest Dr. Ben Lynch’s book Dirty Genes.)
This is one of those supplements I was always eyeing, but never took the plunge because I was spending so much money on supplements already.
But then two things happened: I did a test through Nutrition Genome that said genetically, I am in need of more choline. And then, my doctor ran some tests and discovered I likely have a mold problem, and suggested I supplement with phosphatidylcholine to help my body eliminate the mold.
On top of it, when I am eating a plant-based diet, I am not eating enough dietary choline (especially while pregnant and breastfeeding) because I cannot eat eggs or liver – both of which are top sources of choline.
So… after all that, I decided this was probably a good idea.
Choline comes in a variety of forms, but because my doctor recommended phosphatidylcholine, I decided to use that form. I currently take 1 softgel of BodyBioPC in the morning and another at night.
Supplements I Take When Following a Paleo/AIP Diet
When I am experimenting with a more Paleo or Autoimmune Protocol (AIP) type of diet, which allows for animal foods, I do not need to take the Iron Bisgylcinate, Active B12 with L-Methylfolate, and Phosphatidylcholine supplements I just listed for a plant-based diet.
Instead, I found that there are two specific food-based and animal-based supplements from Heart & Soil that fill in the gaps nicely and give me adequate amounts of all those nutrients. These are:
This is an animal-based organ supplement made specifically for improving iron stores in the blood.
I can easily say this is one of the most life-changing supplements I’ve ever taken. I never knew what real, sustainable energy felt like until I started taking it. It beat out any synthetic iron supplement I’ve ever taken by 1000 times (or maybe even more).
It is the ONLY thing that has increased my iron levels while pregnant which is when I struggle with anemia the most. Even multiple iron bisglycinate pills and iron IVs couldn’t do this!
I take 2-4 capsules of Heart & Soil’s Lifeblood supplement every day, and notice a huge decrease in energy when I don’t.
While the Lifeblood supplement takes care of my need for iron, I need something to help with my folate, B12, and choline intake.
Beef liver just so happens to be high in all of these things! But instead of just stopping at the liver, the Beef Organs supplement from Heart & Soil also adds in beef heart, pancreas, spleen, and kidney to create well-rounded foundational support with a multitude of nutrients.
I take 2-4 capsules of Heart & Soil’s Beef Organs supplement every day.
Okay so that’s it for my nutritional supplements. Now onto Frank.
Frank’s Nutritional Supplements:
Frank takes magnesium, vitamin D/K, calcium, and active B12 with L-methylfolate for the same reasons I do.
He also takes the following:
Also known as activated vitamin B6. Frank originally added this one because of a measured deficiency through a Genova Diagnostics test. Since then, he uses the supplement daily to balance hormones, improve sleep and recovery.
He takes 1 capsule of Seeking Health P-5-P (25mg) daily.
Another deficiency determined through testing, CoQ10 has been a relative breakthrough for stabilizing Frank’s energy and overall function. And when paired with the next supplement, is probably his most notably felt supplement aside from magnesium and Vitamin D/K2.
He takes 1 softgel of NOW CoQ10 (100mg) daily.
PQQ (with some extra goodies)
This one was never on the radar until our oldest daughter had this supplement prescribed to her based on a genetic analysis she had done, which revealed multiple mitochondrial abnormalities.
In order to improve mitochondria generation and function, her doctor prescribed PQQ (Pyrroloquinoline quinone).
Frank looked in the genetic mirror, and considering his own testing, assumed he could benefit similarly. After trying PQQ for a week, he knew it would be a continued maintenance supplement due to stable energy it provided. (We noticed the same effect in our daughter… it seemed to unlock her energy.)
He takes 1 capsule of NOW PQQ Energy daily.
Supplements for Autoimmune Disease to Calm Inflammation & Manage Stress
These supplements are the ones we use to battle the inflammatory symptoms and blood markers that come as a result of autoimmune issues.
Aside from the mushrooms I mention at the end, I am the only one in the house who takes these supplements, especially during these child-bearing years when I find that the hormonal swings from pregnancy, childbirth, and post-partum can cause unexpected inflammation.
Spend any time in the functional medicine/autoimmune world and you’re bound to come across this supplement to calm inflammation, which in turn can reduce pain, improve skin rashes, and more.
Curcumin is a compound in the spice turmeric and is isolated into higher concentrations in supplements. There are over 10,000 published peer-reviewed articles proving turmeric and curcumin benefits.
In regards to autoimmune diseases such as MS, RA, psoriasis, and inflammatory bowel disease, curcumin inhibits these autoimmune diseases by regulating inflammatory cytokines.1
Basically… it’s a powerful substance, and is continuing to become even more powerful as technology advances to make it more readily absorbed by the body.
For me personally, it was a huge help in reducing and pretty much eliminating daily fibromyalgia-like pain and joint pain. I no longer suffer with pain, but still take it to keep inflammation in check especially during stressful times (aka almost every day due to being a mom with young children).
Life-changing. Life-changing, I tell you!
Not everyone has the same experience with CBD oil as I do, but this supplement is crucial to managing my inflammation. Once I learned that our bodies have an endocannabinoid system (commonly referred to as ECS) that modulates our immune function, inflammation, and central nervous system, I was hooked on this idea of using CBD oil.
Why, you ask?
Because CBD oil enhances ECS activity, promoting internal balance within the body, among other benefits.
When I was suffering from chronic, daily pain in my muscles and bones, a dose of 5-10mg of CBD would take it away completely. If I needed a little extra help, CBD paired with Curcumin and Krill Oil was a powerful combination.
I also sleep so much better when I take my daily dose. Some people I know say that it’s effective for their anxiety, too, but I don’t experience that (I wish I did!).
I’ve tried so many brands, and the one that I absolutely love and is most cost effective for our budget (they have sales often) is the Raw CBD by Endoca. I take 5-10mg at night before bed.
If you are looking for more information, this book is really helpful. Endoca also has a lot of useful and easy-to-understand information here. If you scroll down, you can sign up for a free, informational guide.
There are times I try to drop probiotics from my supplements to save money, but it never fails that I always go back to taking them because I feel major benefits during use. What those benefits are? …I can’t really tell you lol. I just know I feel better overall when I take probiotics.
Gut and microbiome health is a huge (possibly THE hugest) factor when it comes to healing autoimmune disease, and prebiotics and probiotics usually make their way into supplement recommendations to help.
There are a lot of myths associated with probiotics and their use for addressing gut dysbiosis, some of which I believed myself for a very long time. I highly recommend this article by Seed Probiotics to clarify their role in modulating your immune system.
The only issue with probiotics is that so many of them are not quality supplements, and may end up doing nothing at all. Over the years, we’ve tried many and were recommended many different kinds and brands by doctors. The two we’ve landed on due to the significant results they’ve provided both to me and the rest of our family are:
Currently, I take Seed Probiotics after a year or two of being on the Just Thrive. The Seed probiotic is a subscription-based program and I only take one capsule a day (instead of the recommended 2) to reduce the cost of subscription.
Black Cumin Seed Oil
This was originally supposed to be a short-term, therapeutic supplement which turned into a daily maintenance supplement. I originally took it because I had a suspicion I was dealing with H. Pylori in my gut and after reading this article by Dr. Izabella Wentz, I decided to try 2 grams a day.
Wow, did it work! I went from daily stomach pain to none at all as long as I took my black cumin seed oil. Then, I had some bloodwork done and found that my thyroid levels were better than they ever have been since weaning off thyroid medication.
From that point on, I decided to stick with it due to its host of other benefits not only for the thyroid, but also the liver, hair, skin, etc. To learn more about its benefits for the thyroid, read this article by Dr. Alan Christianson, and to read more about its other benefits, read this article by Dr. Axe.
I currently take Dr. Mercola’s biodynamic black cumin seed oil – 1 gram in the morning and 1 gram at night.
Adaptogenic Herbs and Mushrooms
Adaptogens are very intriguing for managing autoimmune disease because they help the body naturally adapt to stress… a much better option for your body than coffee when you’re tired, or alcohol when you’re stressed, or junk food when you’re feeling down.
Stress can lead to inflammation (and therefore a worsening of autoimmune conditions), so adaptogens are a healthier way to deal with it.
Adaptogens were a recent addition to our supplementation and I would put them in the category of CBD oil: life-changing.
Since starting our adaptogens, our focus is clear and our energy is stable and lasts all day, even after a night of no sleep. We are also able to calmly deal with anxiety and stressful situations. Very important for raising kids.
However, the reason it took so long to add adaptogens to our supplement protocol was because we tried various brands that gave us no results. It really wasn’t until I started drinking Rasa adaptogenic tea that we both started to feel what true adaptogens can do for the body.
Since then, I’ve settled into a nice routine of drinking 1-2 cups of Rasa daily (they have an AIP version, too!). I prefer it “black” and iced but it took me a few months to get there. It can be an acquired taste.
Frank prefers to take a supplement instead of the tea. He also wanted something to help him stay focused during work so he takes 2 capsules of MycoBotanicals Brain Capsules by Host Defense.
Therapeutic Supplements and Vitamins for Autoimmune Disease
We use therapeutic supplements to address issues that could lead to autoimmune flares or the development of new autoimmune conditions. Examples are: accidental glutening (especially for Frank who has Celiac Disease), viruses, infections, mold exposure, etc.
Consider these more as supplements we keep stocked in our medicine cabinets for “just in case” and acute situations, and those we use to get ahead of a common problem (for us) before it gets worse. We do not use these consistently.
*Dosages of these vary based on whatever we are dealing with. Also, I need to mention that for almost all ailments, we try homeopathy first and many times, that’s all we need. But, we will add these in as supportive measures if needed.
Biocidin products are our favorite for anything virus/pathogen/infection related.
For more information, I found this video/interview with Dr. Terry Wahls very informative.
Leaky Gut Revive®
This powder by Dr. Amy Myers has been instrumental in addressing gut issues as well, especially if there is pain involved. I find it very soothing for the gut lining.
It’s great to have on hand for accidental glutening, gut infections, recovering after food poisoning, etc. Basically, anything that brings gut pain, this is what we turn to.
Another option we like is DGL Plus by Pure Encapsulations.
Ion Biome (previously named Restore) was originally prescribed to us by a local doctor who helped our daughter heal her gut and reverse her food intolerances and allergies.
Given the success we had with her healing, I looked more into the supplement and found how instrumental it can be in sealing a leaky gut and improving tight junction integrity.
Our whole family uses this supplement once a year, along with a few others, to aid in our gut health, but also have it on hand for accidental glutening or other food reactions.
Another favorite for accidental glutening, food poisoning, toxin exposure, and gas/bloating. This is something we keep stocked at all times.
It supports detoxification by binding toxins, and is often used in many of the detox programs we’ve been prescribed by our local functional medicine doctors.
We like the Activated Coconut Charcoal by Dr. Amy Myers.
We keep these on hand for whenever we are eating out or have risk of cross-contamination, or eating treats that may contain some things we don’t eat on a regular basis, such as peanuts and popcorn.
The enzymes are more of a safety net to support the digestive process when dealing with foods our guts aren’t used to. We like these digestive enzymes by Dr. Amy Myers because they contain a protease enzyme that breaks down gluten (many digestive enzymes on the market do not contain this enzyme).
A beneficial yeast helpful for maintaining gut health and in treating gut infections like H. Pylori and mold exposure (it’s helpful for a lot of other things, too, but the gut dysbiosis, H. Pylori, and mold is what we’ve personally had experience with).
Due to the cost of this supplement, we only order it when needed. We like the S. Boullardi by Klaire Labs.
For more information about S. Boullardi, read this article by Dr. Izabella Wentz.
I believe systemic enzymes played a crucial role in my complete reversal of Hashimoto’s Disease and successful third pregnancy. They used to be a maintenance supplement I took for about 2 years. But the price eventually weighed on me and I decided to drop them to see what happens.
So far, I’ve been okay without them, but will consider them should I ever experience an intense autoimmune flare, or when I am trying to get pregnant.
Systemic enzymes are great for cleaning and thinning the blood, reducing scar tissue, managing pain, and breaking down various pathogens and dead material in the blood. They have also been shown to reduce thyroid antibodies, which is why I started taking them in the first place.
I like the Fibrenza brand, and take 2 capsules in the morning and 2 capsules at night on an empty stomach (very important).
For more information, read this article by Dr. Jockers.
Okay, so that is it for therapeutic supplements. There is still one more category of supplements for autoimmune disease I’d like to cover and that is the category of…
Supplements We Would Take If We Could
So far, all the supplements I listed are just the ones Frank and I take. What I don’t mention are the supplements we give to our kids (which is a blog post for another time).
As you can imagine, between us and the kids, the monthly price tag of supplements for our family is hefty, and therefore we have to make cuts somewhere. But, if we did have the extra cash, we would likely add in the following supplements:
Maybe you’ve heard of sulforaphane, a powerful compound found in broccoli sprouts with a whole host of benefits that support detoxification, reduce risk of cancer, protect the brain and, honestly, the list goes on and on because 39 distinct benefits have been found so far… all which can aid in the management and reversal of autoimmunity.
BrocElite is a supplement that offers stabilized sulforaphane in a clinically relevant dose… much easier than making your own broccoli sprouts and hoping you’re getting enough sulforphane in each batch.
But, like I said, because it is possible to get this from food, we choose to make our own broccoli sprouts instead using these seeds, which are tested and selected to contain a large amount of glucoraphanin, a precursor to sulforaphane.
For more information about sulforaphane benefits, listen to this podcast by Chris Kresser where he does a deep dive into the research behind it, plus a step-by-step tutorial on how to grow your own broccoli sprouts at home.
Over the years, I’ve seen a back-and-forth between whether or not glutathione is a useful supplement. Some say it’s not absorbed. Others say it can be absorbed in only specific forms that just so happen to be outrageously expensive.
Glutathione is a critical component in managing inflammation and detoxification, and many people with autoimmunity may find they have low levels of glutathione in the blood (here are some signs you may be glutathione deficient.)
Well! It seems we are finding clarity on the subject, as this study showed that supplementing the reduced form of glutathione does raise levels of glutathione in the blood. Woohoo! And reduced glutathione isn’t insanely expensive… but still expensive enough to not make the cut for our budget, especially because there are other ways to increase glutathione levels.
But if we could, we’d supplement with 1 gram a day of the Jarrow Reduced Glutathione.
And that brings us to the end of this super long post. Whew!
To Recap All of Our Supplements and Vitamins for Autoimmune Disease
Our Daily(ish) Nutritional Supplements and Vitamins for Autoimmune Disease
- Magnesium Glycinate – 2 capsules in the morning and 2 at night (480 mg total)
- Vitamin D/K2 – dosage varies depending on season and sun exposure ranging anywhere from 2,000 IU – 10,000 IU
- Calcium – 1-2 capsules every 1-2 days
When Following a Plant-Based Diet:
- Iron Bisglycinate – 1 capsule daily (25 mg)
- Active B12 with L-Methylfolate – 1/2 lozenge (400 mcg) under the tongue daily
- Phosphatidylcholine – 2 softgels daily
When Following a Paleo/AIP Diet:
- Magnesium Glycinate – 2 capsules in the morning and 2 at night (480 mg total)
- Vitamin D/K2 – dosage varies depending on season and sun exposure ranging anywhere from 2,000 IU – 10,000 IU
- Calcium – 1-2 capsules every 1-2 days
- Active B12 with L-Methylfolate – 1/2 lozenge daily
- P5P – 1 capsule daily (25 mg)
- CoQ10 – 1 softgel daily (100 mg)
- PQQ Energy – 1 capsule daily
Our Supplements and Vitamins for Controlling Inflammation & Managing Stress
- Curcumin – 1 capsule daily (600 mg)
- CBD Oil – dosage varies but is usually 5-10 mg per day of the RAW kind from Endoca
- Probiotics – 1 capsule daily
- Black Cumin Seed Oil – 2 grams daily
- Rasa Adaptogenic Tea – 1-2 cups daily
Our Therapeutic Supplements for Autoimmune Disease
*Dosages for all vary, and these are used for “just in case” or acute situations only.
- Leaky Gut Revive
- Ion Biome
- Activated Charcoal
- Digestive Enzymes
- Saccharomyces Boullardi
- Systemic Enzymes
Supplements We Would Add if We Could
Feeling Overwhelmed About Supplements?
We understand how difficult it is to navigate the supplement world for autoimmune disease. Please keep in mind that the list above came from years of trial and error, working with local doctors, and also listening to practitioners from around the U.S. and globe through podcasts, seminars, health coach training, workshops, and more.
It is unique to us and our needs and budget. Just like our diet, it will ebb and flow as we experiment and learn more as time goes on.
Point is, take your time. Supplements are just that, a supplement to a high-quality autoimmune diet and lifestyle. Once you have the foundation, then you can work with a good functional medicine practitioner to look for unique and common deficiencies, or experiment on your own with common autoimmune-specific supplements.
Go slow and add one at a time until you find the supplementation protocol that works best for you!
- Bright, J. Curcumin and autoimmune disease. Adv Exp Med Biol. 2007; 595:425-51. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3641836/.
LIKE THIS POST? SHARE AND SAVE IT TO YOUR FAVORITE PINTEREST BOARD!
Hi! I’m Anna, co-founder of Healthy Habits Reset. After managing my own autoimmune diseases using lifestyle, habit, and mindset changes, I now work to teach others how to navigate the treacherous and confusing journey of chronic illness living. I firmly believe YOU hold the power to question, think critically, and become your own rock-solid advocate in a world full of unhealthy habits, so you can find the healing you deserve.