Perimenopause and Autoimmune Disease Flares: What’s the Link?

Hormonal shifts in perimenopause add a new layer of complexity to managing autoimmune conditions, especially as women reach this transitional age. Women often enter this phase unaware that the change in estrogen and progesterone can influence immune regulation and trigger more frequent or intense flares. Many notice symptoms that overlap—mood changes, fatigue, joint pain, digestive disturbances. At this crossroads it becomes vital to learn how to manage perimenopause with nutrition, immune support, and hormones.

In this article I share a practical, holistic framework for supporting your body during perimenopause, especially if you live with an autoimmune disease. I present clear steps, perimenopause diet strategies, AIP-friendly food ideas, and natural remedies for perimenopause. I also point to a Take Back Your Health™ podcast episode with deep insights (episode 76 on hormonal balance and immune health) that you can find in the Amy Myers MD YouTube playlist linked here.

How Hormonal Changes Affect the Immune System

During perimenopause, your estrogen and progesterone levels do not simply decline steadily. They fluctuate wildly. Some cycles have high estrogen surges, others have more progesterone deficiency. These swings place stress on immune balance.

Estrogen normally supports certain anti-inflammatory pathways. It encourages regulatory T cells that keep immune responses in check. Progesterone also plays a modulating role, tempering overactive immune responses. When those hormones change erratically, immune control can weaken.

Autoimmune conditions often emerge from immune dysregulation. In perimenopause the hormonal shifts can worsen that dysregulation. Symptoms may intensify or change. Flares may become more frequent or harder to quell. Some women see changes in which organ or tissue is most affected.

Common Symptoms Women May Experience

Hormonal Symptoms

• Irregular menstrual cycles, sometimes with heavy bleeding, sometimes scant

• Hot flashes or night sweats, often waking you from sleep

• Mood changes, increased anxiety, irritability, or low mood

These are the classic symptoms of perimenopause. They can overlap with autoimmune symptom triggers, making it hard to know which is primary.

Autoimmune Symptoms

• Deep fatigue, body aches, joint pain

• Digestive disturbances: bloating, diarrhea, constipation

• Increased frequency of flares in existing autoimmune conditions

You may notice flares that are harder to predict or control than before. Some symptoms may shift in pattern or location.

Key Vitamins and Supplements to Support the Body During Perimenopause

Here are foundational nutrients and support tools that often help during perimenopause in the context of autoimmunity. Always consult your practitioner before beginning new supplements.

Vitamin D

Vitamin D is crucial for immune regulation and bone health. Low levels correlate with more severe autoimmune activity (1). Maintaining vitamin D within optimal range helps moderate immune attack and supports bone density, which becomes more pressing during menopause and as you age. 

Magnesium

Magnesium supports sleep, mood regulation, and muscle and nerve function. Poor sleep and magnesium deficiency can aggravate inflammation. Many women in perimenopause find magnesium helps with restless legs, tension, and sleep maintenance.

Omega-3 Fatty Acids

Omega-3s support cardiovascular health and help reduce inflammation. They support joint comfort and may moderate inflammatory cytokines. Use a clean, high-quality fish oil or algae source.

B Vitamins

B vitamins are essential for energy production and nerve function. They help the body adapt to stress and support methylation and detox pathways. Perimenopause places extra burden on adrenal and thyroid systems, which rely on B nutrients.

Prebiotics and Probiotics

Gut health is foundational to immune balance. Probiotic strains help promote beneficial microbiome members. Prebiotic fiber feeds them. Maintaining gut integrity helps reduce systemic inflammation and autoimmune triggers.

Foods that nourish gut integrity and immune balance (and are AIP compliant) include:

• Bone broth (rich in collagen and amino acids)

• Cooked greens (spinach, chard)

• Sea vegetables (nori, dulse)

• Fermented vegetables (homemade sauerkraut, fermented carrots) - caution if you have SIBO or Candida overgrowth

• Organ meats (if tolerated)

• Fatty fish (wild-caught salmon, mackerel)

• Root vegetables (sweet potato, carrots)
  

Avoiding processed foods, grains, dairy, eggs, nightshades, nuts and seeds initially (consistent with AIP) helps reduce immune triggers.

Does Perimenopause Lower Your Immune System?

Perimenopause does not uniformly weaken immunity as much as it perturbs balance. With decreasing or fluctuating estrogen, the regulatory control over immune responses may loosen. The loss of that hormonal buffer can lead to less tolerance of minor stressors.

Thus immune responses may become more reactive. You may have heightened sensitivity to infections or stronger flares of autoimmune disease. A mild insult that would not have triggered a flare before might now do so. That is why supporting immune resilience becomes a priority during this phase.

Key strategies to bolster resilience include:

• Eating a nutrient-dense, anti-inflammatory diet

• Prioritizing deep, restorative sleep

• Managing stress with mindfulness, breathwork, or gentle movement

• Strength training and low-impact exercise

• Targeted support via supplements (see prior section)

Can Perimenopause Trigger Autoimmune Disease?

It is rare for perimenopause to cause a brand new autoimmune disease by itself. More often it exacerbates or unmasks a latent tendency. If a person already carries genetic or environmental susceptibility, the hormonal shifts can tip the balance toward manifest disease.

Research links estrogen decline with shifts in immune regulation and increased autoantibody formation (2). Some women first notice autoimmune flares in the perimenopausal years. It is wise to monitor new symptoms carefully and work with a practitioner to assess immune markers. Early recognition and intervention improve long-term outcomes.

Learn more about autoimmune diseases, trauma, and psychedelic therapies with Dr. Sara Gottfried on this episode of Take Back Your Health™ podcast.

Integrative Approaches and Professional Guidance

Working with a functional medicine doctor experienced in perimenopause and autoimmune disease is invaluable. This type of provider can order advanced lab testing such as hormone panels, autoantibody profiles, micronutrient panels, and gut health markers to name a few. Then they can actually interpret them and provide a course of action.

Personalized nutrition, elimination diets, and targeted supplementation often yield better outcomes than generic plans. For example, the Perimenopause Bundle is designed to support hormonal balance, immune modulation, and energy during this transition.

This bundle includes:

• EstroProtect for estrogen metabolism support

• Rest & Restore with Melatonin to aid sleep

• Adrenal Support to bolster stress response

• NeuroLive™ to support neurological resilience
  

These supplements complement diet and lifestyle changes, but must be part of a full plan guided by your provider.

You may find inspiration and a deeper understanding in the Take Back Your Health podcast episode, where I explore the interaction between gut health and brain and mental health with Dr. Vincent Padre.

Take Charge of Your Health During Perimenopause

In summary, the hormonal shifts of perimenopause increase the burden on immune regulation. They can worsen autoimmune flares or reveal latent conditions. But you need not passively ride this change.

Focus on foundational supports:

1. Nutrient-dense, AIP-compliant foods

2. Gut health via prebiotics and probiotics

3. Key supplements (vitamin D, magnesium, omega-3, B vitamins)

4. Sleep, stress management, and movement

5. Partnering with a skilled functional medicine provider for labs and personalization

If you would like to explore a protocol tailored to your situation, consider the Perimenopause Bundle at AmyMyersMD.com. Discuss with your provider whether EstroProtect, Rest & Restore with Melatonin, Adrenal Support, or NeuroLive may be right for you.

You do not have to endure escalating symptoms. With education, support, and the right tools, you can take back agency over your health in perimenopause and beyond.