You have endometriosis or adenomyosis. Surgery has been suggested, or you're considering it. You're not sure whether to do it, or whether you've exhausted the non-surgical options first. You want to try a structured root-cause protocol — and then make a more informed decision with real data in hand.
⚠️ This is not anti-surgery framing. For severe disease, surgery may be the right intervention regardless of how well a protocol reduces inflammation. This document is for people who genuinely have time to try a conservative approach first, and who want a structured way to do it.
The "try the protocol first" approach is most appropriate when:
✅ You have 3+ months before you'd need to decide on surgery — symptoms are real but not in a crisis state ✅ You haven't yet tried a structured root-cause approach — maybe you've been on hormonal management (BC, pill cycles) but not on a methylation/clearance/diet protocol ✅ Your imaging hasn't shown severe disease — small endometriomas, no obvious deep infiltrating endometriosis on bowel/bladder/ureter, no severe adenomyotic changes ✅ You're motivated to do daily structured work for 12+ weeks ✅ Your practitioner is open to it — they may want bloodwork, imaging, and check-in points along the way
When it does NOT make sense:
❌ Severe debilitating pain that's already affecting work, sleep, mobility daily — surgery may bring faster relief ❌ Diagnosed deep infiltrating endometriosis (DIE) — particularly with bowel, bladder, or ureteral involvement ❌ Endometriomas > 4 cm — these typically don't respond to medical management ❌ Infertility workup is time-sensitive — surgery may improve fertility outcomes; talk to REI about timing ❌ Acute bowel obstruction, hydronephrosis, or other severe complications — emergencies ❌ You're already at your wits' end — sometimes the right answer is to get the surgery and let the body reset; this protocol can support post-op recovery instead
The honest version of this approach: do the protocol for 90 days, track your data, and have a real decision point.
Follow the Week 1 → Week 4 protocol. This is not "trying it out" — this is the full intervention. Half-measures don't generate clean data.
Track every day:
- Pelvic pain (0–10 scale, morning and evening)
- Heaviness of bleeding (when applicable)
- Fatigue (0–10)
- Sleep quality
- Bowel function
- WHOOP/Garmin recovery + HRV
Bloodwork at Day 0 and Day 30:
- Homocysteine
- hs-CRP
- Vitamin D
- Vitamin B12
- CBC
- CMP including liver enzymes
- Ferritin
- Thyroid panel (TSH, free T3/T4, reverse T3)
Move into Week 4 maintenance. Begin structured food reintroduction. Continue tracking.
Watch for:
- Cycle pain over the next 1–2 cycles vs. pre-protocol cycles — this is your most direct signal
- Food reactions during reintroduction (especially gluten, dairy — common endo triggers)
- HRV baseline shift over the 30-day window
- Pelvic pain trajectory
Continue maintenance. Don't add new variables. Just collect more data points.
Schedule:
- Day 60: practitioner check-in to review trends
- Day 75: optional DUTCH hormone metabolite test if interested in seeing 2-OH : 4-OH ratio
- Day 90: full bloodwork repeat + practitioner consult + decision conversation
At Day 90, you have real data to bring to your surgeon and functional medicine practitioner. Frame the decision as:
Indicators:
- Pelvic pain score average dropped by 30%+ over 90 days
- Cycle pain reduced cycle-over-cycle
- HRV baseline up
- hs-CRP and homocysteine improved
- Fatigue reduced
- Sleep improved
Next steps:
- Continue the maintenance protocol
- Schedule 6-month and 12-month checkpoints
- Surgery can be re-evaluated at the 6-month mark
- Consider DUTCH test annually
- Cyclical 30-day cleanse protocols 2x/year (e.g., spring + fall)
Indicators:
- Some metrics better, some unchanged
- Pain reduced but not eliminated
- Inconsistent cycle improvements
Next steps:
- Look for sticking points: SIBO testing, mast cell evaluation, pelvic floor PT, additional gut microbiome work
- Consider extending the protocol another 90 days with adjustments
- Surgery still on the table at the 6-month mark
- This is a common outcome — protocols work in degrees, not absolutes
Indicators:
- Pain unchanged or worse
- No biomarker improvement
- Cycles same or worse
Next steps:
- This is valuable information. It strongly suggests your specific disease drivers are not primarily inflammatory + hormonal at the level this protocol addresses
- Talk to your surgeon about scheduling
- Going into surgery, you'll be in better physiological shape (sleep, nutrition, autonomic) than you were 90 days ago — which still benefits post-op recovery
- This was not a wasted 90 days; it was an honest experiment that gave you a clear answer
- Reduce inflammatory drive that worsens endo/adeno symptoms
- Improve estrogen metabolism toward safer pathways (2-OH vs 4-OH)
- Restore methylation cycle (if it was bottlenecked)
- Reduce cycle pain in many people whose pain has a strong inflammatory component
- Improve overall energy, sleep, and quality of life
- Build the daily habits that support long-term wellbeing regardless of surgical decisions
- Remove existing endometriotic lesions
- Reverse adenomyotic changes in the myometrium
- Eliminate the need for surgery in severe disease
- Reverse fertility-related anatomic distortion
- Restore reduced ovarian reserve (AMH does not improve from supplements)
- Replace pain medication for severe acute pain
Based on the broader functional medicine literature for endo + the case study evidence in this repo, when people complete a 90-day structured protocol:
- ~25% see major improvement (50%+ reduction in pain, durable cycle improvement)
- ~50% see meaningful improvement (20–40% reduction, partial cycle relief, energy/sleep wins)
- ~15% see small improvement (some wins, but not enough to change surgical plans)
- ~10% see no improvement or worsening (the disease drivers are elsewhere)
You won't know which group you're in until you do it. That's the point of the 90-day window — you generate the data.
Even if you eventually do surgery, doing this protocol first is rarely wasted:
- You enter surgery in a better baseline — lower inflammation, better nutrition, stronger sleep habits, established practitioner relationships
- Your recovery is typically faster — protocols continue post-op (see for-post-surgery.md)
- Your recurrence risk is lower — the protocol you've established can continue to suppress the inflammatory environment that grows new lesions
- You have a personalized food map — you know which foods worsen your symptoms regardless of surgical state
- You have skills — sleep, nutrition, stress management, self-tracking — that serve you beyond endometriosis
This is the strongest argument for the conservative approach: even if you do surgery later, you'll have done better data-gathering for your body in the meantime.
If during the 90-day trial you experience:
- New or worsening severe pain
- Pain that prevents work or sleep
- New bowel or bladder dysfunction
- Hydronephrosis or imaging showing progression
- Severe ovarian endometrioma rupture
- Pregnancy considerations with a clock
Stop the trial and call your surgeon. The protocol is for people who have time to be patient. Some bodies don't have that time, and that's okay.
- Main 30-day protocol README — start here
- Why this works — mechanism
- Week 1 — Foundation — Days 1–7
- Week 4 — Integration — long-term maintenance
- For pre-surgery — if you decide surgery is right at the 90-day mark
- Case Study 001 — the personal context this protocol came from
- Disclosures — full medical disclaimer + affiliate transparency