Inflammation in menopause is one of the most misunderstood challenges women face as they age. Most assume it’s simply an oestrogen issue — but the real story goes much deeper.
Lots of women are simply told to accept a “new normal” of pain, aches, shooting pain, discomfort in their feet, shoulders, and knees. Pain that wakes them up at night when they toss and turn.
Yes, menopause and post-menopause can increase the feeling of pain, but what if the real reason has little to nothing to do with oestrogen? That’s what we want to talk about today.
1. Bacteria-Driven Pain
Years ago, we published an article on septic arthritis, a linked connection between bacteria and pain. Today, more and more research points to three key components of gut microbiome and inflammation-driven pain.
Gut Absorption, Leaky Gut, or Damaged Gut Lining
A damaged or leaky gut lining can affect how well your body holds onto essential micronutrients, minerals, and essential bacteria. This can create a weakened immune system. Common symptoms include:
- Fatigue
- Pain
- Getting sick easily, catching colds/flus or allergies
- Digestive issues
Too Much Bad Bacteria
For instance, elevated levels of certain bacteria strains are characteristic of septic arthritis. These include:
- Staphylococcus aureus — associated with painful skin infections
- Streptococcus species — associated with illness
- Neisseria gonorrhoeae
Too Little Good Bacteria
When dysbiosis is present, two key groups of anti-inflammatory bacteria decline:
Faecalibacterium prausnitzii
This bacteria is not only anti-inflammatory but is also important for fat burning and weight loss. It’s not in a probiotic or yoghurt. It requires prebiotic fibres to grow and thrive.
When it is low, especially at a time when oestrogen is also dropping, it can rapidly increase weight gain, elevate pro-inflammatory cytokine levels, and cause that intense pain.
Clostridium groups IV and XIVa
These are important producers of anti-inflammatory compounds.
Sometimes women only realise there is a gut problem after oestrogen drops. Signs can include:
- Constipation, or conversely, urgency and frequent bowel movements
- Bloating, heartburn, or indigestion
- Food reactions or high histamines/allergies
- Fatigue, especially after eating
- Brain fog
The gut absorption and/or leaky gut symptoms list can look a lot like menopause to many women.
If women go the HRT route, it can help with symptoms at first, but then other things sneak in or don’t get addressed, most commonly weight gain, skin issues, or ongoing digestive problems.
The first trigger in the Cycle of Metabolic Inflammation we discussed a couple weeks ago, is the gut and/or immune system. 80% of the immune system sits in the gut, so the trigger could have been a significant illness, EBV, or CV-19, or a prolonged drop in essential micronutrients.
For instance, it is common to see a drop in Vitamin D as progesterone drops in a woman’s forties, which can activate gut pathways and cause dysbiosis.
2. Genetic Pathways Breaking Down
Changes in hormones can activate underlying genetic vulnerabilities.
Without knowing it, you could be experiencing:
- A drop in a key micronutrient,
- A deficiency in an amino acid, or,
- A need for a specific type of probiotic bacteria you didn’t know to look for, let alone the name of it!
Oestrogen is an anti-inflammatory and insulin-sensitising hormone. It helps balance the LDL to HDL ratio right up until menopause. It also plays a role in regulating leptin, our satiety “hunger” signalling hormone. The oestrobiome also helps balance the gut microbiome, so genetic vulnerabilities affecting bacteria absorption, acid balance, or histamine levels can all influence the immune system downstream.
Under the surface, oestrogen and progesterone quietly support:
- Cholesterol
- Blood pressure
- Metabolism
- Detoxification pathways
- Immune function
- Digestion
- Joint lubrication
- Bone mineralisation and stabilisation
When oestrogen drops, it is often our epigenetics’ response to menopause and post-menopause that really kicks in.
Pain is often one of the early inflammation responses, because oestrogen had been running cover for these genetic vulnerabilities all along.
3. Detoxification Malfunction
The liver, gallbladder, cholesterol metabolism, and blood pressure all play a significant role in the strength or weakness of your detoxification pathways. When these pathways are compromised, the following nutrients can be very low:
- B12, B6, and Folate
- Vitamin D
- Zinc and Copper
You could have great genetics. You could have sailed through your forties without any dramas. You could have little to no problems with your immune or digestive systems. And yet still have problems with detoxification pathways.
Detoxification challenges are actually the most common pain trigger we see, especially after menopause.
When oestrogen drops, you can really feel pain if you have:
- High oxidative stress
- High levels of arachidonic acid
- Building insulin resistance
- Thick or sluggish bile flow
It’s also worth looking beyond “normal” blood work results, or simply attributing symptoms to high cholesterol, high blood pressure, or weight gain around the middle.
Weight around the abdomen is typically insulin-resistant weight sitting on the organs. Research is showing that in some patients, the body begins to treat this visceral fat as though it were an organ and it actively produces pro-inflammatory cytokines (IL-6 and TNF-alpha), which proliferate pain, especially joint pain.
Detoxification malfunction is so common that in our very first treatment consultation with a patient presenting with pain issues, it is where we begin looking on pathology. Many of our patients report an 80% to 90% drop in joint pain within a month of starting treatment.
If you have underlying genetic mutations, gut dysbiosis, or an autoimmune diagnosis, the continued lowering of oestrogen, even well past 60 and 70, can probe and amplify pain, because of how the detoxification pathways respond to the absence of oestrogen that had been running cover all those years.
For women with conditions like osteoarthritis or rheumatoid arthritis, for instance, they could actually be taking oestrogen and still experience pain.
Unpacking and decreasing inflammation in menopause is a crucial part of feeling great again. Pain is our body’s way of asking us to get curious, investigative, and to become our own nutrition biohackers.
Learn More: Watch Our Free Webcasts
We are really passionate about helping women understand why pain and/or arthritis flare up during hormonal shifts. This is one of the most uncomfortable long-term challenges after menopause for women.
If you would like to learn more about inflammation in menopause, we have two webcasts that take you down each path:
- If the gut component resonates with you, watch the full webcast: Bacteria, Inflammation & Peri/Post Menopause
- If you feel you have a number of other inflammatory symptoms you can’t identify, watch the full webcast: Genetic Activation during Peri/Post Menopause
Both presentations have recently been updated, so even if you’ve seen them before, they now unpack more than our 2025 and earlier versions.
If you would like support with your symptoms, we also offer a free introductory consultation. Please organise a time with us here.
We hope you found this helpful. We look forward to connecting with you soon.
Warmly,
Tiaan & Carrie
