pregnant women with notebook and ultrasound picture with text overlay - Pregnancy and Autoimmune Disease: [Part 2] How I'm Managing My Autoimmune Disease While Pregnant

How I’m Managing My Autoimmune Disease While Pregnant

Anna Autoimmune Disease & Pregnancy, Autoimmune Mom (& Dad) Life, Living Well with Autoimmune Disease Leave a Comment

This is Part 2 of my Pregnancy & Autoimmune Disease Series.  The other posts in this series include:

Part 1: How I Proactively Prepared for a Healthy Pregnancy

Part 3: First Trimester Update: Coping with Symptoms & Saying Goodbye to Hashimoto’s Disease

Part 4: 2nd & 3rd Trimester Update: Battling Anemia, Restless Legs, & Hip Pain

Part 5: Third Baby Birth Story – 2 Weeks Overdue

pregnant woman holding notebook, pen, and ultrasound picture with text overlay - Pregnancy and Autoimmune Disease: How I'm Managing My Hashimoto's & Other Autoimmune Conditions While PregnantIf you haven’t already read Part 1 which explains how I prepared for this pregnancy, please do so before reading this post, otherwise… some things I talk about might not make sense.  You can read it by clicking the link below:

Part 1: How I Proactively Prepared for a Healthy Pregnancy

Okay.  Great!

So, I’m just going to pick up right where I left off in Part 1.  Which is… I got pregnant.  But, before I get into what my plan is for managing this pregnancy, I want to show you something I learned from my other two pregnancies and that is: pregnancy tends to suppress my autoimmune issues.

(For some women, it’s the opposite and their autoimmune issues get worse.  This is why it’s so SO SO important to work with a knowledgeable doctor/specialist before and during an autoimmune pregnancy.)

To illustrate my personal experience, I took this graph below from my post about how I reduced my Hashimoto’s thyroid antibodies from over 2000 to almost zero.

linear graph showing downward trend of thyroglobulin antibodies

Notice the drops in thyroglobulin antibodies during both my first and second pregnancies.

Here’s a summary of the numbers:

Before First Pregnancy:  136

During First Pregnancy:  23

Before Second Pregnancy:  113

During Second Pregnancy:  56

This was not drug induced.  I didn’t do anything different with my diet or lifestyle.  The only difference was that I was pregnant.

And now, with my third pregnancy:

Before Third Pregnancy:  16

During Third Pregnancy:  5

(My thyroid peroxidase antibodies are negative.  They have been for awhile.)

What’s interesting about my situation is even though I had an increase of thyroid antibodies after my first pregnancy, that was not the case for my second.  After I delivered my second baby, my thyroid antibodies went even lower, but that’s also when I developed a bunch of other autoimmune antibodies.  Lol.  So… not sure how I feel about that.

My point is…

My Hashimoto’s (and possibly my other autoimmune conditions) are suppressed during pregnancy. 

This kind of excites me.  Not only because I feel really good (once the morning sickness wears off), but also because I have a 9-month(ish) long opportunity where my immune system is naturally suppressed. 

That, to me, sounds like an awesome time to focus on nutrition, gut-healing, stress-reduction, etc. not only for the health of my baby, but also to help my body heal as much as possible in order to prepare for post-partum, which is when the risk of a flare increases big time.

Those of us who experience the wonderful remission of symptoms from our autoimmune diseases during pregnancy, often have them come back with a raging vengeance after delivery.  I’m hoping that optimizing my health during pregnancy will lead to a healthy baby, delivery, and minimize the chance of a super-flare. 

Maybe I can even come out of this without any autoimmune symptoms again!  You never know…

Anyway, here’s my plan for managing my autoimmune disease(s) while pregnant.

**Please remember this is not medical advice!  I am not a doctor, medical expert, or practitioner.  This information cannot be use to diagnose or treat any condition or disease.  I strongly advocate for working with a knowledgeable healthcare team before, during, and after pregnancy, especially if you have an autoimmune disease.

First, my team of doctors and practitioners.

Due to my remission of symptoms and low antibodies without the use of any immune-suppressant or disease modifying drugs, my pregnancy is NOT considered high risk like many autoimmune pregnancies are.  However, that does not mean we’re not keeping an eye on everything.

I am currently working with 3 medical doctors and 3 “alternative” medical practitioners.  They are:

Medical Doctors:

  • My OBGYN.  He’s awesome, and his major focus is to keep everything as natural and low intervention as possible while keeping me and the baby safe.  He’s also particularly interested in making sure I do not hemorrhage again / need a blood transfusion after delivery.
  • A functional medicine/holistic primary care doctor.  He checks my thyroid levels and various nutritional markers (vitamins, minerals) every other month throughout the pregnancy to ensure my body, and the baby, is adequately supported.
  • An integrative/functional medicine doctor who is very familiar with autoimmune disease and pregnancy.  He takes the place of a rheumatologist on my healthcare team since my pregnancy isn’t considered high-risk (and I’ve actually never worked with a rheumatologist before).  I’m working with this doctor in particular to develop my post-partum plan so I don’t flare after delivery.

Alternative Medicine Practitioners:

  • I love me some acupuncture!!  Always have (since the day I tried it), and always will.  My acupuncturist specializes in fertility and pregnancy, so… extra bonus.  I go for an appointment every month.  I used to go twice a month, but I don’t think my body needs it that frequently at this point.
  • I am not sure where I’d be today without my chiropractor(s).  Especially during pregnancy.  Last pregnancy, my hips shifted so bad that I could not walk, bend over, or really do anything (pain-scale was at an 8).  One or two adjustments and boom, back to normal.  The best.  I receive adjustments once a month, or as needed if I have a crazy hip situation.
  • I work with a homeopath occasionally throughout the year to address random issues, pregnancy included.  I’ll talk a little more about this in a bit.

This team gives me major confidence in managing my pregnancy.  My medical doctors especially are all more “holistically” minded, but also willing to use pharmaceuticals or other interventions when absolutely needed.  The best of both worlds. 

So, while I’m trusting my doctors to keep an eye on things I might miss or don’t understand, here’s what I’m doing in my daily life:

My Diet

About 1-1.5 years ago, I used The Autoimmune Protocol to help reverse my post-partum autoimmune symptoms from my second pregnancy.  I am still on a version of that diet, but it’s more personalized to avoid my unique food sensitivities and includes non-compliant foods I don’t seem to have issues with. 

The foods I avoid under all circumstances are:

  • Gluten
  • Dairy
  • All grains
  • Tomatoes (I tolerate all other nightshades)
  • Eggs
  • Walnuts and Flaxseed (I’m fine with all other nuts/seeds)
  • All processed/junk foods, artificial dyes, flavors, preservatives, etc. These foods are usually eliminated anyways based on my above restrictions.

But, perhaps what’s more important about the foods I avoid are the foods I eat on a daily basis.  I follow a few self-made guidelines and they are:

  • A huge emphasis on raw foods, particularly vegetables. I aim for 8 cups of raw vegetables a day (this includes fermented and homemade pickled veggies).  I also try to include 2 servings of fresh or frozen fruit per day.
  • I severely limit roasted foods, including roasted meats and vegetables because I’ve found I do not tolerate them well… like at all.
  • Due to limiting roasted foods, I also limit all cooking oils, even the “healthy” ones.  The only oil I eat daily is cold olive oil, usually in homemade salad dressings or pesto.  I don’t really have an amount I aim for, but I consume olive oil daily.
  • I still eat cooked foods, but the majority are steamed or boiled vegetables, starches (potatoes, yucca, plantains) and grass-fed/pasture-raised meat.  On occasion, I will eat properly prepared (soaked and pressure cooked) beans.
  • Healthy fats in the form of olives, avocados, nuts, and seeds.
  • While I don’t necessarily limit or set a maximum amount of meat, I find that if I fill my plate with vegetables and eat those first, I only need a small portion of meat/fish/seafood before feeling satisfied.  I feel better when I consume less meat in comparison to what I used to eat, which was mostly meat and very little vegetables.
  • I drink AT LEAST 96oz of water a day, and will slowly work my way up as the pregnancy continues.

This is the diet that works well for me, at this moment.  It might change (it’s always changing), but I don’t foresee that happening any time soon since it keeps my autoimmune issues from flaring.


Natural Dessicated Thyroid

I use Westhroid Pure.  This is the only “prescription” drug I’m on for this pregnancy due to my Hashimoto’s Disease, and I don’t use it every day.  Honestly, it’s driving me crazy.

As I mentioned in Part 1, right before I got pregnant, I experienced this massive wave of thyroid healing within just one month’s time.  It was totally unexpected, and I am so happy about it, but I would be MUCH happier about it if it wasn’t happening while I was pregnant!!

I know how important optimal thyroid levels during pregnancy are, especially for the baby. My past two pregnancies were optimally supported.  I took thyroid hormone every day and monitored my levels every 4-6 weeks.  I had peace of mind and it was easy to just pop the thyroid pill in my mouth every morning, knowing it provided what my body and the baby needed.

But now, I’m on this rollercoaster.  The pregnancy started off fine.  I could take ¼ grain per day without any hyperthyroid symptoms.  I thought that’s where I’d stay… or maybe I would need to increase it.

Well, that dose only lasted for about a month, until I started to show overdose symptoms (with blood tests to prove I was going in that direction). 

So, I reduced to every other day.  It didn’t take long until the overdose symptoms returned again.

Finally, I went to every other OTHER day, and that worked… until it didn’t.

**I did this while working with my doctor.  Weaning off thyroid medication is a delicate process ESPECIALLY while pregnant, and it requires the oversight of a knowledgeable doctor.  Please never attempt this on your own!

So now, I’m waking up every day, wondering if my thyroid is fully healed and capable of producing enough hormones for me and the baby.  I wonder if my occasional tired feeling is because I didn’t sleep well, or because I’m pregnant and growing another person, or if it’s because my body doesn’t have enough thyroid hormone in it to function. 

Thankfully, I’m working with my doctors on this.  Both my OBGYN and primary care doctor monitor my thyroid levels often enough (every 4 weeks or so) to give me peace of mind. 

So far, my levels remain in optimal range despite pretty much stopping my thyroid medication/only taking it when I feel my body needs it.  We will see what happens in my second trimester, when the demand for thyroid hormone seems to be greater, at least for me based on my blood tests from past pregnancies.

As for now, I just need to listen to what my body is telling me, and continue working with my doctors / testing to make sure everything is looking okay.

Prenatal Vitamins

Prenatals are tough for me because there is always something about them that doesn’t work well with my body. 

First, no matter which prenatal I choose, I am always so nauseous after taking them during the first trimester.  It doesn’t matter if its with or without food, or what time of day it is.  I haven’t taken prenatals consistently during the first 12(ish) weeks of my pregnancies for this reason. 

I figure it’s better for me to support my body through nutritious food, rather than throw up my prenatal (and therefore my food).  Eventually this passes and I’m good to go by the second trimester.

But then I run into another problem… I’m really sensitive to the type and amount of B Vitamins.  I can only tolerate methylated B Vitamins due to my MTHFR genetic variations, but… not too much of them.  The problem for me is that so many prenatals have way more than I need.

The common amount of methylated folate, for example, is 800-1000 mcg.  I can only tolerate, at most, 400 mcg.  I also eat cups and cups of greens/vegetables every day and feel comfortable I am obtaining the amount of naturally occurring folate I need from diet alone.

So, that leaves not too many options… in fact, it leaves me no options (that I have found) in terms of being able to take a full/recommended dose.  My compromise is to take ½ a dose of the prenatal I tolerate best, which is Seeking Health’s Prenatal, and eat as nutrient dense as I can to fill in the rest.

During the first trimester, I use the chewables, which have a lower amount of vitamins/minerals/etc. than the capsules, because it’s all I can get down.  During the second, when I’m feeling better, I switch to the capsules.  I’ve tried the protein powder form and really liked it but it breaks me out in hives.  I think probably because it contains rice protein, which I eventually found I’m sensitive to.

Various Vitamin/Mineral Supplements

Even with a nutrient-dense diet and prenatals, I still need supplementation for a few things based on blood tests and my diet restrictions.  They are:

  • Iron Bisglycinate– Pregnancy drains me of iron (particularly my ferritin or iron reserves).  I needed an iron IV during my first pregnancy.  I don’t think this pregnancy will be as bad.  This brand/form does not give me an upset stomach.
  • Magnesium – I take magnesium even when I’m not pregnant. This is something my body needs, and I cannot get enough through diet alone.  Without it, I develop tremors and muscle spasms.  It also helps prevent those crazy calf and feet cramps that make you hop out of bed in the middle of the night.  This is the brand/form I use.
  • Choline – Choline is an essential nutrient for pregnancy, but many women don’t get enough… I’m probably one of them. Eggs are one of the best sources of choline and I can’t eat eggs.  Liver is the next highest source, and even though I eat it every week, I can only stomach so much.  So… I take choline in supplemental form.  (If you’ve never heard of this crucial nutrient before, especially for pregnancy, check out this article.)
  • Vitamin D (when needed) – Just like magnesium, I take Vitamin D even when I’m not pregnant. Over the years, I’ve realized this is something I can’t go without.  I supplement heavily in the colder months when I don’t see much sun, and much less in the summer months.  I take this one because it contains both Vitamin D and K2, which work together.  My levels are continuously monitored by my doctor. 

Food Supplements

  • Dessicated Liver (pasture-raised) – I almost consider liver like a multivitamin. It’s SO nutrient dense, and includes ample amounts of beneficial nutrients for pregnancy like choline, vitamin A, B12, trace minerals, and iron.  I don’t eat nearly enough, so I take 4-6 capsules of desiccated liver daily.  Since taking these, I haven’t needed as much iron supplementation as I have in past pregnancies.
  • Fish oil – fish oil is a heavily recommended supplement for all pregnant women due to its EPA/DHA content.  Usually, I eat enough sardines, anchovies, and salmon so I don’t feel the need to supplement, but fish grosses me out during pregnancy and therefore… I don’t eat it as often.  I take 2 caps daily to make sure I’m providing what my body needs.


There are so many reasons I take probiotics:

  • Probiotics support a healthy gut microbiome, which is crucial for managing and recovering from autoimmune disease.
  • My baby then inherits my gut bacteria, and the last thing I want is my little babies developing autoimmune disease due to my possible gut dysbiosis.
  • I learned that despite having a birth plan, I still have very little control over how the birth of my baby is going to go.  I never expected a post-partum hemorrhage during my second delivery, or all of the drugs and blood transfusions that came with it.  By supplementing with probiotics, and keeping up with my supplementation and nutrient dense diet, I’m building up my defenses so those types of traumatic events aren’t such a big blow to my body if they happen.
  • And… I just feel better when I take them.

The probiotics I take are MegaSpore and these ones by Garden of Life.  I also eat fermented foods like sauerkraut and coconut-milk yogurt.

Systemic Enzymes and MegaIgG2000

I go into more detail about why I take these supplements in Part 1, so I won’t elaborate much here.  But, in short:

  • Systemic enzymes help cleanse the blood, detoxify the body, reduce inflammation, and modulate the immune system.
  • MegaIgG2000 (serum-derived bovine immunoglobulins) contains the most abundant antibody found in the body and can bind to various environmental toxins, pathogens, viruses, etc., allowing the immune system to safely remove them from the body.

**I should mention that while I plan to take systemic enzymes for the duration of the pregnancy, I am only using the IgG supplements for the first 12 weeks due to cost.  I then plan on reintroducing them shortly before and after giving birth to help keep things calm while my body goes through all the post-partum changes.


I know I already called this one out during my healthcare team section, but it really deserves its own little place down here.  These remedies relieve so many of my pregnancy symptoms.  For real.  No amount of supplements, herbs, or whatever else can do what these can do!  But the biggest benefit here is that they keep me away from OTC drugs, which carry many risks.

So, for example:

  • Heartburn – like the kind that makes you so uncomfortable you want to throw up.  Easily relieved with just one dose of Natrum Phos 6X.  Gone within minutes.
  • Crazy calf cramps – they strike in the middle of the night and there is nothing you can do to relieve them because your muscles are so rigid.  I’ve had cramps go on for minutes.  Frank usually rushes downstairs and either grabs the BioPlasma or the Mag Phos 6X.  Just one or two pellets and my muscles relax within seconds.  Literally seconds!  Not exaggerating at all here.
  • Insane migraines – During my second pregnancy, I had one giant migraine that lasted for weeks.  But one dose of Sepia 30c every morning took care of the pain until the migraine passed for good.

Homeopathy for the win!! 

(If you don’t know what homeopathy is, then go read about it here!  Homeopathy has changed my life and my family’s life.)


This one might seem like a “duh,” but I think it is key for managing autoimmune disease while pregnant.  The first 12 weeks for me are like walking uphill, against a flowing river, with chains weighing me down lol.  It makes sense – I’m making a person.

So, this pregnancy, I decided to prioritize sleeping and rest over other things, like dishes, cleaning the house, and even blog work (which is why I’m publishing this post when I’m already 15 weeks pregnant.)

This isn’t easy when I have two busy toddlers running around, but if I ignore my body’s obvious cry for rest, I place an immense and unnecessary stress on myself.  Stress can lead to hormonal imbalance, causing issues with adrenals, thyroid (which I’m of course trying to avoid!), pituitary glands, etc. 

Not only is this detrimental for anyone trying to recover from autoimmunity (rest, adrenal “resets, or balancing hormones are usually part of autoimmune recovery programs), but it’s not healthy for the baby either.  The last thing I want is my body trying to manage all of this dysfunction when its focus should really be on providing for the baby.

A healthy body = a healthy pregnancy = a healthy baby.

And that’s my ultimate goal.  A healthy baby with no complications.  As much as I want to manage my autoimmune diseases, my main goal has been, and always will be, to make sure I prevent autoimmunity in my children using the knowledge I’ve learned over the past decade.

The truth is: I might flare after this.  The diet, supplements, rest, and everything else I’m doing might not actually prevent the return of my autoimmune issues.  But, I have hope because I believe in the body’s ability to heal.  I’ve experienced it over and over again in my quest to reverse my Hashimoto’s and I have no doubt that even if this birth and delivery doesn’t go as planned, I CAN recover.

If you’re curious to see how it’s all going, read my first trimester update:

Click here to read My First Trimester Update: Coping with Symptoms & Saying Goodbye to Hashimoto’s Disease


pregnant woman holding notebook, pen, and ultrasound picture with text overlay - Pregnancy and Autoimmune Disease: How I'm Managing My Hashimoto's & Other Autoimmune Conditions While Pregnant

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