Last Chance - Mother's Day Sale

Last chance - Mother's Day Sale

For moms, thyroid health matters. Save $25 on our thyroid test kit or self-pay membership using code MOMDAY.

How to Manage an Autoimmune Disease Flare Up

Strategies to manage a difficult autoimmune flare-up.
How to Manage an Autoimmune Disease Flare Up
Last updated:
Medically Reviewed by:

In this article: 

  • Autoimmune diseases of the thyroid
  • What is an autoimmune flare-up?
  • Common triggers of a flare-up
  • Strategies for managing thyroid flare-ups

There are more than 80 types of autoimmune diseases that affect the body, including the thyroid gland. An autoimmune disease occurs when the body's natural defense system cannot tell the difference between its cells and foreign cells. Consequently, the immune system begins to attack healthy cells in the body. It's not clear what causes this response in the body. Still, many researchers believe it is a combination of genetic and environmental factors and may be prompted from an infection or injury. 


Autoimmune diseases of the thyroid


The most common cause of hypothyroidism in the United States is Hashimoto's thyroiditis. Hashimoto's is an autoimmune disorder where the body produces antibodies that attack the thyroid. This attack causes the thyroid to slow down and no longer produce the essential hormones the body needs for energy and metabolism.

Common symptoms of Hashimoto's disease include:

  • Paleness or puffiness of the face
  • Constipation
  • Difficulty getting pregnant
  • Hair loss or thinning, brittle hair
  • Irregular or heavy menstrual periods
  • Depression
  • Slowed heart rate


The most common cause of hyperthyroidism is Grave's disease, another autoimmune disorder. In this disease, the body produces antibodies that attach to the thyroid and chemically turn it on, causing the thyroid to produce too many hormones. Consequently, the body's metabolism speeds up.

Common symptoms of Grave's disease include: 

  • Anxiety and irritability
  • Tremor of your hands or fingers
  • Heat sensitivity and an increase in perspiration or warm, moist skin
  • Weight loss, despite regular eating habits
  • Enlargement of your thyroid gland (goiter)
  • Change in menstrual cycles
  • Erectile dysfunction or reduced libido
  • Frequent bowel movements
  • Bulging eyes
  • Fatigue
  • Thick, red skin usually on the shins or tops of the feet
  • Rapid or irregular heartbeat (palpitations)

What is an autoimmune flare-up?


An autoimmune flare-up is a period of worsening and intensification of symptoms due to an added stressor (even something minor) on your already compromised immune system. Symptoms of a Hashimoto's flare-up are generally those already seen with the disease. Only, they tend to be much more severe. 


Each person experiences a flare-up differently. Some patients have described it as feeling "tired, sore, and beat up," "an absolute dragging fatigue," and "utter exhaustion." A flare-up may present a large number of symptoms at a moderate intensity level, or maybe just a few signs at a debilitating level.


Thyroid care online

Dealing with Hypothyroidism?  Video chat with a thyroid doctor

Get answers and treatments in minutes without leaving home - anytime. Consult with a U.S. board certified doctor who only treats hypothyroidism via high-quality video. Insurance accepted.

Common triggers of a flare-up


Patients often report that it is hard to distinguish between a Hashimoto's flare-up versus a flare-up of another autoimmune condition. Some people even attribute their symptoms to their menstrual period or episodes of mental and emotional strain. Studies suggest that flare-ups are most commonly the result of some form of physical, mental, or emotional stress on the body


Physical stressors may include:

  • Viral or bacterial infection or illness
  • Lack of sleep
  • Nutritional deficiencies
  • Surgery
  • Hormonal imbalance
  • Menstruation
  • Excessive physical strain or exertion
  • Childbirth
  • Other health conditions


Mental and emotional stressors may include:

  • A significant change such as moving, a career change, or divorce
  • Grief, such as loss of a loved one
  • Depression
  • Anxiety
  • Post-traumatic stress or traumatic life events like an accident


While it is hard, or even impossible to prevent specific triggers of an autoimmune flare-up, there are strategies to help manage the triggers that may be preventable. Keeping a log of your daily habits, meals, and emotional health around the time of a flare-up can be an excellent tool for identifying your triggers. 


Strategies for managing thyroid flare-ups 

Reduce stress

Stress is one of the leading causes of autoimmune flare-ups. Studies have found that long-term stress can have damaging effects on every system in the body. Cortisol is the "stress hormone" that activates your body's fight-or-flight response. Not only does it increase your heart rate and blood pressure, but it drains your energy supplies and increases your blood sugar. Furthermore, cortisol alters the way your immune system works and prevents your tissues from being repaired. 

Your body's response to stress should be a short-term reaction to keep you safe. However, when cortisol levels remain high for long periods, these effects can aggravate symptoms related to autoimmune disease.   

Try to identify ways that you can reduce the amount of stress in your life. For example, politely say "no" to extra activities or additional responsibilities. Self-care is an incredibly powerful tool to lower cortisol levels, so practice daily relaxation techniques such as yoga, meditation, journaling, and stretching. 


Eat a nutrient-rich diet

A healthy diet is essential if you are working to prevent autoimmune thyroid flare-ups or are currently having a flare-up. There is more and more evidence that suggests that a healthy diet is critical for thyroid health. The Standard American Diet tends to be poor in nutritional value. It can lead to a deficiency of many essential nutrients. Nutrients that support optimal thyroid functioning include vitamin D, selenium, iron, iodine, and zinc. Deficiency in these nutrients may lead to a thyroid flare-up, and you can monitor your vitamin levels with an essential vitamin blood test.

Certain foods can aggravate autoimmune conditions, and many of those foods make up the "western diet."

Foods that may cause an autoimmune flare-up include:
  • Processed foods
  • Grains
  • Legumes
  • Dairy products
  • Refined sugar


Eating a thyroid-friendly diet can help reduce inflammation and decrease the severity of flare-ups. Try to eat meals that mostly consist of lean meat, fish high in omega-3's, and vegetables. Some studies suggest that eating a gluten-free diet may also help people with autoimmune thyroid conditions like Hashimoto's.

Daily Thyroid Care


The reinvented multivitamin that works smarter to help fill the gaps in your thyroid health journey
Learn More
Vegan and free of gluten, GMOs, dairy and iodine

Finally, many people have food sensitivities that can increase inflammation in your system. Following a strict elimination diet such as the Autoimmune Protocol (AIP diet), followed by a gradual reintroduction of foods, may help you find foods that trigger your autoimmune reactions.   


Low impact movement

We know that physical exercise is already challenging with thyroid conditions. When you have a flare-up, likely, you won't want to exercise at all. And we get it - you are likely already exhausted and may be suffering from severe joint and muscle pain. But gentle, low impact exercises can help improve fatigue and musculoskeletal pain, even in a flare-up. 

Studies suggest that people with autoimmune conditions need regular physical activity, even in the presence of severe symptoms. If you are having a thyroid flare-up, try gentle exercises such as yoga, stretching, and gentle walks. These types of exercise can improve joint mobility, boost your mood, and make you feel better. Even light activities can produce more oxygen and nutrients available to your organs. They can also release mood-boosting neurotransmitters - dopamine, norepinephrine, and serotonin.  


Get enough sleep

Make sleep a high priority in your life, even when you are not suffering from a thyroid flare-up. When we sleep, our body performs critical housekeeping processes that keep us functioning well. Sleep helps with restoring tissues, improving communication between neurons, processing memories, replenishing energy stores, and releasing hormones. Another critical role of sleep is to flush toxins out of your body, which may help prevent flare-ups as toxins may aggravate autoimmune diseases. 

It can be hard to get quality sleep when you are having a thyroid flare-up, even when you are completely exhausted. Try some of the following tactics to improve your sleep during a flare-up:

Practice good sleep hygiene

Turn off your screens at least an hour before bed. Wind down from your day with some self-care practices like a warm bath to soothe your joints, gentle stretching, meditation, journaling, reading, or having your partner give you a massage. 


Prepare your sleep environment

If you suffer from one temperature extreme or the other, adjust the thermostat to your comfort. Similarly, use the right bedding to keep you comfortable. 

Dress for success

Wear layers to bed if your internal thermostat jumps from hot and cold throughout the night.

Avoid certain foods at night

Spicy foods can cause night sweats and heartburn. Similarly, caffeine and sugary foods and drinks (like alcohol) can cause insomnia. 

Set a bedtime

Try to go to bed at the same time so that your body gets used to falling asleep at a specific time. Research suggests that most adults need 7-9 hours of sleep. Your sleep requirements may increase during a thyroid flare, so you may need to give yourself more time to sleep during flare-ups. 

Take your medication

In many cases, hypothyroidism requires medication. Therefore, it is essential to take your medicine every day and as instructed. Sometimes, thyroid medication must be adjusted to meet your specific requirements, even if you have been taking the same dose for many years. If you need help finding the right dose of thyroid medication, meet with a thyroid doctor to help you keep your thyroid symptoms in check.  

A note from Paloma Health

Flare-ups can be truly debilitating and can hinder everyday life. Taking steps to manage your physical, mental, and emotional health can help decrease the severity and length of a flare-up. If you suffer from thyroid flare-ups, our team of thyroid doctors and thyroid nutritionists are here to help you feel better—faster.


Share article:

Julia Walker, RN, BSN

Clinical Nurse

Julia Walker, RN, BSN, is a clinical nurse specializing in helping patients with thyroid disorders. She holds a Bachelor of Science in Nursing from Regis University in Denver and a Bachelor of Arts in the History of Medicine from the University of Colorado-Boulder. She believes managing chronic illnesses requires a balance of medical interventions and lifestyle adjustments. Her background includes caring for patients in women’s health, critical care, pediatrics, allergy, and immunology.

Read more

Is Paloma Right For Me?

Hypothyroidism is a long-term commitment and we’re committed to you. Schedule a free, no-obligation phone consultation with one of our intake specialists to find out more.

Schedule a call
thyroid hormone for hypothyroidism

Find out if Paloma is right for you. Schedule a free call with one of our health care advisors.

Schedule a Call