Low Progesterone Protocol

Progesterone is the dominant hormone of the luteal phase (the second half of your menstrual cycle). It is produced by the corpus luteum, a temporary gland formed from the ovulated follicle. Progesterone is essential for regulating cycles, supporting fertility and early pregnancy, balancing estrogen, improving sleep, calming the nervous system, and stabilizing blood sugar.

If you are not ovulating consistently, or if the quality of the ovulated egg is poor, your corpus luteum will not produce enough progesterone. This is one of the most common hormonal imbalances in cycling women today.

Common Signs of Low Progesterone

• Short luteal phase (less than 11 days)

• Spotting before your period

• PMS, mood swings, anxiety, or poor sleep

• Fertility challenges or early miscarriage

• Low body temperature in the luteal phase

• Irregular or anovulatory cycles

• Estrogen-dominant symptoms (heavy bleeding, breast tenderness, bloating)

Why It Happens (Root Causes)

Low progesterone is typically the result of a deeper imbalance rather than the problem itself. In cycling women, two main issues drive it:

1. Lack of Ovulation

If ovulation does not occur, progesterone cannot be produced. Many women experience anovulatory cycles even if they bleed monthly. Ovulation is a finely tuned process controlled by the brain, ovaries, and environment. Disruptions in that system can easily shut it down.

Common causes include:

• Low energy availability: Under-eating, over-exercising, or fasting too aggressively can suppress GnRH (the brain signal that initiates ovulation). Use the Cronometer app to determine if you are meeting your daily energy needs based on your activity level. Testing leptin can also be helpful, as it will be low during times of scarcity, indicating insufficient nourishment or fat reserves to prioritize fertility and progesterone production.

• Chronic stress: Elevated cortisol can blunt the LH surge that triggers ovulation. Both under-eating and over-exercising can contribute to high cortisol levels. Blue light exposure, particularly at night, is another major driver of cortisol elevation in the modern world.

• Thyroid dysfunction: Both low and high thyroid function can disrupt ovulation.

• High prolactin: Often caused by stress, certain medications, or pituitary issues. Elevated prolactin suppresses GnRH signaling.

• Insulin resistance or PCOS: Follicles may fail to mature and release an egg.

• Micronutrient deficiencies: Low levels of vitamin D, magnesium, zinc, B6, vitamin C, or selenium can impair reproductive signaling.

2. Poor Egg Quality

You can ovulate and still have low progesterone if the egg quality is poor or the corpus luteum is weak. Egg health determines how well the corpus luteum functions, how much progesterone it produces, and how long production is sustained.

Egg cells are the most mitochondria-dense cells in the body. These mitochondria generate the energy required for ovulation, fertilization, and hormone production. Mitochondrial dysfunction caused by oxidative stress, toxin exposure, nutrient deficiencies, or circadian disruption leads to immature eggs and inadequate progesterone output.

3. Mitochondria: The Starting Point for Progesterone

Every molecule of progesterone is created inside your mitochondria. The first step of hormone production occurs here:

• Cholesterol must be transported into the mitochondria by a protein called StAR.

• Inside, the enzyme CYP11A1 converts cholesterol into pregnenolone, often referred to as the “mother hormone.” Pregnenolone is produced in response to natural light exposure during sunrise, a critical time when progesterone is naturally low. It may take 3–4 months of consistent circadian rhythm support to notice changes in progesterone levels.

• Pregnenolone then exits the mitochondria and is converted into progesterone. However, if the body is prioritizing cortisol production due to stress, pregnenolone can be diverted to make cortisol instead, reducing progesterone potential.

If there is insufficient cholesterol, impaired pregnenolone production, or poor mitochondrial energy (ATP) output, progesterone synthesis will slow down even if ovulation occurs.

4. Cell Membrane Health: The Hidden Foundation

While mitochondrial function is the main driver of hormone production, cell membrane health also plays a significant role in progesterone physiology. The membrane influences how cells receive signals, import cholesterol, and respond to LH.

Why this matters:

• Cholesterol transport: Membrane receptors bring cholesterol into the cell. If the membrane is rigid or damaged, cholesterol uptake decreases.

• LH signaling: LH receptors sit on the membrane. If the membrane is disordered due to inflammation or poor diet, the ovary may not respond properly.

• Intracellular trafficking: Cholesterol must move between the endoplasmic reticulum and mitochondria. Poor membrane fluidity slows this process.

• Corpus luteum function: After ovulation, rapid cholesterol uptake depends on a healthy membrane.

How to support membrane function:

• Eliminate industrial seed oils (canola, soybean, safflower, sunflower, corn).

• Eat omega-3-rich foods (sardines, salmon, anchovies, flax).

• Include omega-6 seeds like pumpkin, sunflower, and flax daily for balanced membrane composition.

• Eat phospholipid-rich foods (egg yolks, liver) to support membrane structure.

• Reduce toxin exposure (alcohol, heavy metals, other toxic chemicals).

• Support antioxidant defenses with colorful vegetables, selenium, and vitamin E. Use Cronometer to track how much of these nutrients you are getting daily.

How to Assess It

Confirm ovulation:
Use LH strips, basal body temperature (BBT), and cervical mucus tracking. A post-ovulation temperature rise of about 0.5°F or more indicates progesterone activity.

Check progesterone:
A mid-luteal blood test (about 7 days after ovulation) is the most accurate but only captures a single day. Many women have normal results despite low overall luteal progesterone production.

Real-world tip:
I personally struggled with low progesterone after seven years on birth control, even though my bloodwork appeared normal and my DUTCH test showed “low-normal” results. The most helpful tool was Inito strips. By tracking progesterone metabolite levels daily from ovulation until my next period, I discovered that progesterone stayed consistently much lower than estrogen. This provided a much clearer picture of my hormonal rhythm than a single test ever could.

Other labs to consider:

• TSH, free T3, free T4 (thyroid function)

• Prolactin (should not be elevated)

• Leptin (should not be low)

• 25-OH vitamin D (target sufficiency; anything below 30, especially in summer, indicates low sun exposure)

• Fasting insulin, glucose, C-peptide (if PCOS is suspected)

• LH:FSH ratio and androgens (to assess ovulatory function; a high LH:FSH ratio suggests insulin resistance and PCOS physiology, while a low ratio with low androgens may indicate hypothalamic suppression)

Order labs here:

• Basic thyroid panel
• Prolactin
• Leptin
• Fasting insulin, fasting glucose, HbA1c
• C-peptide
• Progesterone, estradiol, testosterone, DHEA-S
• FSH and LH
• 25-OH vitamin D 
• Serum magnesium
• Comprehensive metabolic panel
• CBC with differential
• Lipid Panel

The Hormone Hierarchy: Adrenals, Thyroid, and Sex Hormones

If adrenal or thyroid function is impaired, sex hormones will always struggle to normalize. The body prioritizes survival over reproduction. Typically, the order of dysfunction looks like this:

• Adrenals: Chronic stress, trauma, or poor sleep leads to dysregulated cortisol. (Refer to my masterclass Beyond Adrenal Fatigue for more details on root causes and foundational support.)

• Thyroid: Metabolic slowdown follows adrenal depletion, lowering cellular energy output.

• Sex hormones: Reproductive hormones are downregulated as a final adaptation.

Supporting adrenal resilience through stress reduction, circadian alignment, nutrient support, and adequate rest, as well as optimizing thyroid function, are crucial steps for restoring healthy ovulation and progesterone production. Without addressing these upstream systems, sex hormone protocols often fail to work fully.

Lifestyle Reset Steps

1. Support Regular Ovulation (The Foundation)

• Eat enough: Aim for at least 30–35 kcal/kg body weight daily if under-fueled. Do not restrict carbohydrates long-term. Use Cronometer for more accurate tracking, especially if you are active.

• Train smart: Avoid excessive high-intensity exercise. Focus on resistance training and walking. If your recovery is slow, you may need to slow down. 

• Manage stress: Use daily stress-reduction practices such as breathwork, journaling, or time outdoors. Find enjoyable activities. I personally started knitting and find it very relaxing.

• Align your circadian rhythm: Get morning sunlight and dim artificial lights two hours before bed. Invest in blue-blocking glasses, ideally with red lenses, for evening use.

• Address thyroid and prolactin: Refer to available protocols or work with your practitioner.

2. Restore Mitochondrial Health (Egg Quality and Hormone Output)

• Light: Watch the sunrise daily and reduce blue light exposure at night for at least 3–4 months, though this should become a lifelong practice.

• Fuel production: Include whole-food carbohydrates and adequate calories. Long-term low-carb diets can lead to low thyroid function and low progesterone.

• Key nutrients (pay attention to Cronometer readings for some of these):

  • B vitamins for energy production

  • Magnesium for ATP synthesis

  • Copper and iron for the electron transport chain

  • CoQ10 for mitochondrial function and egg quality

  • Cholesterol from eggs, butter, and seafood as raw material

• Reduce mitochondrial toxins: Avoid alcohol, mold, heavy metals, and chronic toxin exposure. Consider drainage support. 

• Mineralize water: Add a pinch of natural salt to water and ensure potassium and magnesium intake to support membrane potential and mitochondrial charge.

3. Eat to Build Hormones

• Three balanced meals per day: Avoid constant snacking to stabilize hormones.

• Protein: 1.2–1.6 g per kg of body weight daily.

• Healthy fats: Include cholesterol and omega-3 fats daily.

• Omega-6 seeds: Consume one serving daily of pumpkin, sunflower, or flax seeds to support membrane integrity and hormone balance.

• Whole-food carbohydrates: Include seasonal fruits, root vegetables, beans, and intact grains. Depending on the season and your activity level, you may tolerate more carbohydrate-rich meals.

• Antioxidants: Eat a wide variety of colorful vegetables and fruits to reduce oxidative stress.

• Avoid: Fried foods, processed seed oils, and trans fats.

4. Key Nutrients for Progesterone Support

Targeted Supplements (Optional)

Once lifestyle and nutrition foundations are in place, targeted support can help accelerate results:

If you have PCOS:

• Myo-Inositol by Pure Encapsulations: 2 g twice daily – improves testosterone levels and insulin sensitivity (check the insulin resistance protocol, as this is very common in PCOS)

If you have oxidative stress:

• N-Acetylcysteine (NAC) by Pure Encapsulations: 600 mg 2–3 times daily – may increase egg quality by reducing oxidative stress

• CoQ10 by Needed: 600-1200 mg/day with fat – supports egg quality by improving mitochondrial energy production and reducing oxidative stress

• Melatonin by Quicksilver: 3-6 mg 1 hour before bed – may improve egg quality and slightly increase IVF pregnancy rates (important to support circadian rhythm for optimal natural melatonin production). Long-term use isn’t recommended; based on studies, around 45 days is an effective duration.

If you have high prolactin:

• Vitex: 20–40 mg/day of Vitex as Ze440 (not available in US) or 1-2 capsules of Vitex Extract by Integrative Therapeutics– may reduce prolactin and support luteal progesterone

If you have low nutrient intake (based on Cronometer, labs, or symptoms):

• Vitamin D3: Dose to reach sufficiency (30+) while aiming for at least 20 minutes of direct sun exposure daily.

• Magnesium

• B complex (some brands I like are Seeking Health and Thorne)

• Prenatal multivitamin if multiple nutrients continue to be low (I like Needed)

NOTE: These supplements often need at least 3 months of consistent use before you’ll notice meaningful changes.

When to Consider Natural Progesterone Support

If you have addressed ovulation, mitochondrial function, membrane health, nutrition, adrenal and thyroid function, and your progesterone levels remain low, the next step is to explore natural progesterone supplementation.

Topical or oral natural progesterone can be used strategically in the luteal phase to restore balance, support fertility, and relieve symptoms. This should always be done carefully and with proper timing. A complete guide to natural progesterone use is available for download alongside this protocol: Progest-E Guide.

Retesting and Tracking Progress

Monitor your progress every 2–3 cycles:

• Cycle tracking: Confirm ovulation with LH surge, BBT, and mucus changes.

• Luteal phase length: Aim for 12–14 days.

• Mid-luteal progesterone: Target above 10 ng/mL.

• Symptom improvements: Track changes in PMS, spotting, mood, sleep, and energy.

✅ Key Takeaway for Members

You do not fix low progesterone by taking a pill. You rebuild it by creating the internal environment where hormone production thrives. That means:

• Supporting ovulation with proper nutrition, stress management, and circadian alignment

• Restoring mitochondrial health so your cells can produce pregnenolone and progesterone

• Building healthy cell membranes to improve hormone signaling and cholesterol transport

• Supporting adrenal and thyroid function so reproductive hormones can thrive

• Eating nutrient-dense foods with enough cholesterol, omega-3s, and omega-6 seeds

• Using targeted supplements strategically to accelerate progress

• Considering natural progesterone support only if deeper work is not enough

When these foundations are in place, progesterone often rises naturally, and symptoms resolve as your cycle returns to balance.

 💬 Community Discussion Only

Comments here are meant for sharing feedback, insights, or experiences with other members. Paola does not respond to questions here, but she reads everything and may occasionally pop in to share additional knowledge or refine protocols based on community feedback.

📍 For direct questions or support with applying this protocol, please post inside the Inner Circle Q&A instead.