You Thought HRT Would Make It All Better. But It Hasn't.
By Krystle Alves | Naturopath, Nutritionist & Yoga Therapist | B.HSc, Adv. Dip. Naturopathy
You did the thing you were supposed to do. You went to your GP, described the symptoms the broken sleep, the brain fog, the mood that turns on a dime, the exhaustion that no amount of rest fixes and you walked out with a prescription. Hormone replacement therapy. The thing that was supposed to put you back together.
Maybe it helped a little. Maybe it helped at first. But something still isn't right. You still don't feel like yourself. And nobody has a good explanation for why.
Here's what most people aren't being told: perimenopause is not an estrogen problem. Not entirely. And if the only thing being addressed is estrogen, it's no surprise the results are incomplete.
Perimenopause Is a Whole-System Hormonal Shift Not Just an Estrogen Drop
The standard story goes like this: estrogen declines, symptoms appear, replace the estrogen, symptoms resolve. It's a tidy narrative. It's also too simple.
The hormonal changes of perimenopause begin years sometimes a decade before your final period, and they involve far more than estrogen.
Progesterone drops first. This is one of the most underappreciated facts in perimenopause. Progesterone begins to decline in your mid-to-late 30s, well before estrogen makes its exit. Progesterone is your calming hormone it supports sleep, stabilises mood, counterbalances estrogen's stimulating effects, and has a direct influence on the GABA receptors in your brain (the same receptors targeted by anti-anxiety medications). When progesterone drops, sleep becomes lighter, anxiety edges in, and you find yourself lying awake at 3am with your mind running. Many people start HRT years after this shift has already happened, meaning a piece of the puzzle was already missing long before treatment began.
Estrogen doesn't just fall it fluctuates wildly. In early perimenopause, estrogen often spikes unpredictably before it begins to decline. This means some symptoms breast tenderness, heavy periods, mood swings can actually be signs of excess estrogen fluctuation, not deficiency. Adding more estrogen into this picture without addressing those fluctuations can sometimes amplify symptoms rather than resolve them.
FSH rises. Follicle-stimulating hormone (FSH) climbs as the brain tries harder to signal the ovaries to produce more estrogen. Elevated FSH is associated with its own set of cognitive and mood effects that are often conflated with estrogen deficiency symptoms.
Cortisol increases. Research from the Swiss Perimenopause Study confirms that cortisol your primary stress hormone rises progressively through the perimenopausal transition. This matters because cortisol and the sex hormones share a precursor pathway. A body under chronic stress will preferentially direct resources toward cortisol production, leaving less available for estrogen, progesterone and testosterone. If stress is high and the nervous system is dysregulated, HRT is working against an upstream current.
Insulin sensitivity shifts. Estrogen plays a role in how well your cells respond to insulin. As it fluctuates and declines, blood sugar regulation becomes less stable even in people who have never had issues before. This can show up as energy crashes, sugar cravings, weight changes around the midsection, and worsening brain fog. HRT does not directly address insulin resistance.
Thyroid function is affected. Thyroid disorders particularly Hashimoto's thyroiditis can emerge or worsen during perimenopause. The immune system changes that accompany the hormonal shift can trigger or amplify autoimmune activity. Thyroid symptoms overlap significantly with perimenopause symptoms: fatigue, low mood, weight changes, cognitive slowing, cold intolerance. If thyroid function is compromised and going unaddressed, HRT will not fix it.
Estrogen Works Like a Fire Blanket and When It's Gone, What Was Already Simmering Will Flare
This is the framing that I think matters most, and the one that most clearly explains why HRT doesn't always solve everything.
Estrogen is an extraordinarily potent anti-inflammatory hormone. It modulates immune function, protects the brain, supports the gut lining, regulates the HPA (stress) axis, and exerts a dampening effect on systemic inflammation. For decades, this anti-inflammatory blanket has been quietly suppressing things that were already there low-grade gut issues, autoimmune tendencies, nervous system dysregulation, underlying inflammation without either of you knowing it.
When estrogen withdraws, the blanket lifts. And whatever was simmering underneath begins to surface.
This is why perimenopause can feel like a sudden onset of multiple, seemingly unrelated conditions all at once. It's not that menopause caused them. It's that estrogen was masking them and now it isn't.
This is also why two people with identical hormone levels can have wildly different symptoms. The difference isn't their hormones. It's what was already there underneath.
Replacing estrogen may partially re-drape the blanket. But if the fire underneath the gut dysbiosis, the chronic nervous system activation, the autoimmune burden, the mitochondrial depletion is never addressed, the symptoms will persist through it.
The Hormone Nobody Is Talking About: Testosterone
If estrogen is the hormone everyone is focused on, testosterone is the one being almost entirely ignored in women's health despite having a profound effect on how you feel, think and function.
Testosterone begins declining in women from around age 30. By the time perimenopause arrives, levels may already be significantly lower than they were a decade earlier. And yet routine testing rarely includes it, and it's infrequently offered as part of standard HRT protocols for women.
Here's what testosterone actually does in the female body:
Energy and vitality. Low testosterone is strongly associated with fatigue that doesn't improve with rest the kind of bone-deep tiredness that makes everything feel like an effort. Research shows this is one of the most prevalent symptoms in the perimenopausal cohort, with 96% of perimenopausal and menopausal women in one large study reporting fatigue or lack of energy. Testosterone is a significant contributor here and is rarely the first thing investigated.
Brain function. A 2024 pilot study found that transdermal testosterone therapy was associated with approximately 43% improvement in cognitive complaints memory problems, difficulty concentrating, mental foginess. A separate study found that low testosterone relates to poorer cognitive function in women, particularly in those carrying the ApoE-ε4 gene variant. If brain fog is part of your picture and it hasn't budged on estrogen alone, testosterone is worth examining.
Mood and motivation. The same research found a 47% improvement in mood in women who received testosterone therapy. Testosterone supports dopamine pathways the drive, reward and motivation circuitry and its absence can produce a flat, low-motivation, "what's the point" quality that doesn't respond particularly well to estrogen or progesterone.
Muscle mass and metabolic function. Testosterone is anabolic it supports lean tissue, bone density and metabolic rate. As it declines, you may find it harder to maintain muscle despite consistent training, and easier to gain weight despite no obvious dietary change. This isn't a willpower issue. It's a hormonal one.
Libido. This is the one everyone knows about. But it's worth noting that testosterone's effect on libido is not just about desire it's also about responsiveness, sensation and energy for intimacy. These effects are distinct from those of estrogen.
Testosterone in women requires careful assessment testing timing matters, results need to be interpreted in clinical context, and any intervention should be individualised. But ignoring it altogether means managing perimenopause with an incomplete picture.
What I Look at in My Perimenopause Patients Beyond Hormones
After years of working with people in perimenopause, the pattern I see repeatedly is this: the hormonal changes are real and significant. But they are never the whole story. They are the match and what determines how big the fire gets is everything else that was already in place.
Here's what I consider alongside hormonal status:
The HPA axis and cortisol. A dysregulated stress system upstream of the sex hormones will undermine hormone therapy. I look at how someone's body is responding to stress sleep quality, morning energy, afternoon crashes, response to minor stressors as a window into HPA axis function. If the nervous system has been running in a sympathetic-dominant state for years, perimenopause will tip it over. Supporting the nervous system is not optional here; it's foundational.
Thyroid function, including antibodies. I routinely check TSH, free T3, free T4 and thyroid antibodies (TPO and TgAb). Standard testing often stops at TSH, which can appear normal even when the thyroid is under autoimmune attack and conversion of T4 to active T3 is impaired. Perimenopause is a known trigger point for Hashimoto's emergence or exacerbation.
Gut health and the estrobolome. The gut microbiome contains a specialised set of bacteria the estrobolome that directly regulates how estrogen is metabolised and recirculated. Poor gut health impairs this process, contributing to estrogen dominance, worsening PMS-like symptoms in perimenopause, and potentially increasing the risk of downstream conditions. I look at digestive symptoms, bowel patterns, history of antibiotic use, and where relevant, functional stool testing.
Blood sugar regulation. Unstable blood sugar drives cortisol, worsens sleep, accelerates inflammation and amplifies almost every perimenopausal symptom. I pay particular attention to energy patterns through the day, sleep onset and maintenance, and any history of metabolic concerns. Dietary adjustment in this area can make a significant difference to symptom load.
Nutrient status. Magnesium, B vitamins (particularly B6 and B12), zinc, iron and vitamin D are all commonly depleted in the perimenopausal transition and all play important roles in mood, energy, cognitive function and hormonal metabolism. Deficiencies here can mimic or amplify hormonal symptoms in ways that are often missed because they aren't being looked for.
Sleep architecture. Perimenopause disrupts sleep at the level of sleep architecture it's not just that night sweats wake you. Progesterone decline reduces slow-wave (deep) sleep. Cortisol dysregulation affects the natural cortisol awakening response. Addressing sleep as a system, not just a symptom, changes outcomes.
Lived stress load and nervous system history. I always want to understand what was happening in the years before perimenopause symptoms became obvious. A history of chronic stress, trauma, burnout, or sustained high output is highly relevant not as a psychological observation, but as a physiological one. The nervous system carries a load, and perimenopause makes that load visible.
The Takeaway
HRT can be a genuinely useful tool. For some people, it's transformative. I'm not here to argue against it.
But if you are on HRT and still not feeling well, it's worth asking: what else is in the picture that hasn't been addressed? Replacing one hormone in a system where multiple hormones are shifting against a background of stress, gut disruption, thyroid changes, blood sugar instability, and nutrient depletion will often produce a partial result.
The question isn't "why isn't HRT working?" The question is: "what else needs attention?"
That answer will be different for every person. And finding it requires looking at the full picture, not just the hormones on a standard panel.
This post is for educational purposes only and does not constitute medical advice. If you are experiencing symptoms of perimenopause, please consult a qualified health practitioner for personalised assessment and support.
Krystle Alves is a naturopath, nutritionist and yoga therapist with over 17 years of clinical experience. She works with clients experiencing burnout, fatigue and complex health concerns, including people navigating perimenopause who have been told their results are "normal." Consultations are available via telehealth Australia-wide. Book a consultation →
References:
Schaefer EKE et al. (2021). Steroid Hormone Secretion Over the Course of the Perimenopause: Findings From the Swiss Perimenopause Study. Frontiers in Endocrinology. PMC8712488
Dhanvijay S et al. (2025). Endocrine and Metabolic Mechanisms Underlying Fatigue in Perimenopausal Women. IJSAT. Link
Neves J et al. (2024). Effect of transdermal testosterone therapy on mood and cognitive symptoms in peri- and postmenopausal women: a pilot study. PubMed. 39283522
Crestani CC et al. (2024). Low testosterone levels relate to poorer cognitive function in women in an APOE-ε4-dependant manner. PMC. PMC11151480
Prevalence of Cognitive and Mood-Related Symptoms in a Large Cohort of Perimenopausal and Menopausal Women. PMC. PMC11738833