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If you take thyroid medication and bioidentical hormones but still feel tired, foggy, or like the scale won’t budge, you’re not alone. Menopause and perimenopause change how your body handles hormones. Not just estrogen and progesterone, but thyroid hormones too. These shifts can make thyroid labs swing, symptoms persist, and treatment feel unstable even when labs look “normal.”
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Perimenopause and menopause aren’t single events. They’re processes. In perimenopause, ovarian hormone production becomes erratic. Estrogen can spike, crash, and spike again. Those rapid swings create symptoms like hot flashes, anxiety, insomnia, and brain fog. They also change how your body handles thyroid hormones.
Here’s what’s happening: estrogen affects thyroid-binding globulin (TBG), the protein that carries thyroid hormones in your blood. When estrogen rises, TBG increases and binds more thyroid hormone, leaving less free hormone available to your tissues. When estrogen drops, TBG falls and free hormone rises. So rapid estrogen changes mean fluctuating thyroid hormone availability, and fluctuating symptoms, even if your meds and blood tests haven’t changed at all.
Once menopause settles in, average estradiol from the ovaries falls and stays lower. The adrenals step in to produce more estrone, a weaker estrogen. That shift changes the steady-state of hormone balance and often reduces overall thyroid requirements. In other words, many people need less thyroid medication after menopause. If dose adjustments aren’t made, continuing an unnecessarily high dose can create problems that look like either over-treatment or, paradoxically, under-treatment (weight gain, fatigue, hair thinning) and cause long-term risks to bone, heart, and brain health.
HRT is a helpful tool for many people, but the form and route matter for thyroid function.
Key Insight: Treat HRT decisions and thyroid dosing as linked. Any major change in one often warrants attention to the other.
Some micronutrients support liver-based hormone processing and thyroid conversion pathways. They aren’t magic fixes, but they help your system fine-tune hormone availability and elimination. This is especially important when hormones are swinging during perimenopause or changing with HRT.
Molybdenum is a trace mineral that supports sulfur-containing amino acid pathways in the liver. These pathways are critical for hormone metabolism, conjugation, and elimination. When estrogen levels fluctuate or when you’re using exogenous hormones, your liver has extra work to do. Molybdenum is a cofactor in several detoxification steps that help the liver “buffer” hormone inputs and keep levels steadier.
Selenium is essential for proper conversion of T4 into active T3 and for processing reverse T3 into metabolites like T2. It also protects thyroid tissue from free radical damage caused by iodine processing. In short, selenium helps your thyroid make and manage active hormones while limiting oxidative stress.
A few practical notes on selenium: dietary selenium is safe, and Brazil nuts are a reliable food source. One or two nuts daily can supply meaningful selenium without likely causing excess. Supplemental selenium should be dosed thoughtfully. A sensible range is roughly 50–150 micrograms per day, with an upper practical limit near 300 micrograms. Regularly exceeding that top end risks toxicity. Remember that both dietary and supplemental selenium contribute to your daily intake, so count both.
Not all supplements are neutral. A few common ingredients can worsen thyroid symptoms or interfere with treatment. Pay attention to labels. Some “energy” or “adrenal” products include elements that cause trouble.
Synthetic vitamin B6 (pyridoxine HCl) is widespread in multivitamins, energy drinks, and adrenal blends. Pyridoxine HCl must be converted in the body to the active form (pyridoxal-5-phosphate, or P5P). Excess pyridoxine can accumulate and cause neuropathy, numbness, anxiety, tremors, and worsening hot flashes. If you have unexplained neurological symptoms, check serum B6. High levels of pyridoxine can be the culprit. If you need B6 supplementation, prefer P5P (active B6).
High-dose manganese is another one to watch. The body needs manganese in tiny amounts, but supplemental doses above about 3–5 milligrams per day have been linked to lower thyroid function. Most people get adequate manganese from food. High supplemental doses can actually act as thyroid suppressants.
When ovarian estrogen production declines, the adrenals pick up much of the slack by making estrone and other intermediates. Healthy adrenal function smooths that transition. Unhealthy or stressed adrenals magnify hormonal instability.
There are simple, evidence-friendly habits that support adrenal rhythm and improve how your body uses thyroid hormones and responds to estrogen shifts:
These steps don’t replace medication or hormone management, but they make your body better able to use the hormones it has, both natural and prescribed.
Because menopause, perimenopause, and HRT changes affect thyroid hormone binding and conversion, timely lab testing is essential. When anything significant changes (starting or stopping HRT, changing the route of estrogen, or altering your thyroid medication) plan to recheck thyroid labs and reassess symptoms.
Useful labs include:
How often should you test? If you start or stop HRT or change thyroid dosing, recheck labs in 6–8 weeks initially, and again at 3 months or whenever symptoms change. If you’re stable, routine monitoring every 6–12 months is reasonable depending on your clinician’s guidance.
Here’s one confusing reality I see all the time: being on too much thyroid hormone can create symptoms that look like hypothyroidism, and the reverse is true. Bone, heart, and brain health suffer from chronic over-treatment. On the other hand, continuing a too-high dose once estrogen falls after menopause can produce fatigue, weight gain, and hair loss (classic hypothyroid complaints) because the whole hormonal context changed.
That’s why careful retesting and symptom-focused adjustments are key. Don’t treat labs alone. Treat the person, and expect doses to change across life stages.
Here’s a step-by-step approach to stabilize thyroid and sex hormone balance during perimenopause or menopause:
Contact a clinician experienced with thyroid and menopausal medicine if you have new or worsening fatigue, weight gain, hair loss, or brain fog despite “normal” labs. The same goes for neurological symptoms like numbness, painful extremities, tremors, or severe anxiety, especially if you use B6-containing supplements. If you’re starting or stopping HRT and need guidance about timing and lab checks, or if you suspect over- or under-treatment that isn’t responding to simple adjustments, it’s time to get expert help.
Menopause and perimenopause change how your body handles thyroid hormones. Rapid estrogen swings in perimenopause create fluctuating thyroid-binding globulin and variable hormone availability. Once you’re in menopause, overall thyroid needs often fall as ovarian estradiol drops and the adrenals make more estrone.
Here’s what helps: expect dose adjustments when you start, stop, or change HRT. Retest thyroid labs 6–8 weeks after a change. Support hormone metabolism with selenium and molybdenum, but avoid excessive or problematic supplement forms, especially pyridoxine HCl and high-dose manganese. Prioritize adrenal-supporting habits like morning bright light, a protein-containing breakfast within an hour of waking, consistent sleep, and stress reduction. And work with a clinician to individualize care. Labs, symptoms, and life stage are all part of the picture.
Menopause doesn’t have to mean erratic symptoms or unstable thyroid control. With the right testing, thoughtful supplement choices, attention to HRT routes, and lifestyle rhythms that support adrenal and liver function, you can stabilize hormone balance and feel significantly better during this transition.

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Dr. Alan Glen Christianson (Dr. C) is a Naturopathic Endocrinologist and the author of The NY Times bestselling Hormone Healing Cookbook, The Metabolism Reset Diet, and The Thyroid Reset Diet.
Dr. C’s gift for figuring out what works has helped hundreds of thousands reverse thyroid disease, heal their adrenals, and lose weight naturally. Learn more about the surprising story that started his quest.