How Restoring Your Missing Period Can Fix Low Ferritin, Iron, and Folate in Hypothalamic Amenorrhea
Before we dive in, we want to give credit to the author. This was written by Cat, a graduate of our Holistic HA Practitioner (HHAP) Certification Program. Cat brings a deep understanding of the root causes of HA and is passionate about supporting women on the path to recovery through education, empowerment, and holistic strategies.
Low Ferritin with No Period? Here’s Why Restoring Your Missing Period Actually Helps
When living with hypothalamic amenorrhea (HA), many women notice abnormalities in their bloodwork such as low ferritin, folate, and sometimes iron. (1,2) This can feel confusing, especially if you’re not experiencing regular menstrual bleeding, which is the most common reason for low iron in women. (3) Understandably, this can lead to worry: “If I start bleeding again, won’t my iron stores drop even further?” The surprising truth is the opposite. Restoring your menstrual cycle actually creates the hormonal environment your body needs to rebuild ferritin and restore nutrient balance. Let’s dive in!
Ferritin, Iron, and Folate: How They Work Together
Iron is the raw material your body uses to make hemoglobin, the oxygen-carrying part of red blood cells. Ferritin is the storage protein that holds iron reserves, like a warehouse and folate, a B-vitamin required to build DNA and red blood cells, coordinates where and how the iron is used throughout the body (like a project manager). These nutrients are deeply interconnected. When ferritin levels are low, it is usually a signal that iron stores are low too. Without enough iron or folate, red blood cell production suffers, leading to fatigue, weakness, and impaired recovery. (4)
The Misconception About Bleeding and Iron Loss
It is true that very heavy periods can sometimes contribute to low iron. But in HA, the problem isn’t iron loss — it’s most likely a lack of sufficient iron intake paired with and exacerbated by low reproductive hormone production, preventing you from absorbing and using iron properly. Restoring your period doesn’t drain ferritin — it helps your body replenish it.
Why Might They Be Low in HA?
Even though women with HA often don’t menstruate, several factors can drive low ferritin, iron, and folate. Particularly in HA, a lack of nutrient dense food intake, intense exercise, a high level of stress and the resultant hormonal impairment all contribute to lower ferritin and thus iron reserves. (2)
Dietary Restriction and Gut Function: A Dual Impact on Ferritin:
In hypothalamic amenorrhea (HA), dietary restriction and gut health challenges often go hand in hand, both contributing to low ferritin and iron status. Restrictive eating patterns—whether intentional (e.g., dieting, eliminating food groups) or unintentional (e.g., under-fueling relative to activity level)—reduce the intake of iron-rich foods and critical cofactors like vitamin C, folate, and vitamin B12 that support iron absorption and utilization. Over time, this limits the body’s ability to build and replenish ferritin stores. (2,5)
At the same time, chronic stress and undernutrition can negatively affect gut function. Low energy availability impairs intestinal barrier integrity and alters the gut microbiome, leading to reduced nutrient absorption efficiency. 6 Additionally, disordered eating patterns or overuse of high-fiber/low-energy foods may bind iron in the gut and further limit absorption. (7) Gastrointestinal symptoms commonly reported in HA, such as bloating, constipation, or slowed motility, can also compromise the uptake of nutrients—including iron and folate. (8)
Together, reduced dietary intake and impaired gut absorption create a “double hit” against ferritin levels. Even if some iron is consumed, it may not be effectively absorbed or utilized.
Suppressed Estrogen:
One of the defining features of hypothalamic amenorrhea is chronically low estrogen. While most people associate estrogen only with reproductive function, it is actually a systemic hormone that influences many aspects of metabolism, nutrient regulation, and blood health. (9)
Specifically, estrogen directly influences iron homeostasis. Research shows that estrogen helps regulate hepcidin—the hormone that controls whether iron is stored or released for use. Animal and human studies demonstrate that estrogen suppresses hepcidin activity, which improves iron bioavailability. When estrogen is low, hepcidin regulation becomes less efficient, leaving iron “locked away” in storage and ferritin levels lower than expected. (10,11)
In addition, estrogen supports gut health and nutrient absorption. It influences gut motility, microbiome composition, and intestinal barrier integrity, When estrogen is chronically low, the gut may become less efficient at absorbing key nutrients, including iron and folate, (12) adding another layer to the deficiency risk in HA.
Cortisol, Stress, and Elevated Hepcidin:
In hypothalamic amenorrhea, chronic psychological stress, under-fueling, and overtraining keep the body in a state of “fight or flight.” One major outcome of this is elevated cortisol, the primary stress hormone. While cortisol is useful in short bursts—helping mobilize glucose and fuel muscles during acute stress—chronically high cortisol disrupts multiple body systems, including iron metabolism. (13)
High cortisol increases the production of pro-inflammatory cytokines. These cytokines stimulate the liver to release hepcidin, the master regulator of iron balance. Hepcidin acts like a “gatekeeper”: when it rises, it blocks the export of iron from intestinal cells and macrophages into the bloodstream. (14) This means that even if you eat iron-rich foods, your body struggles to absorb and mobilize them effectively.
This process can mimic the pattern seen in anemia, where iron is present in the body but unavailable for red blood cell production because it is locked away in storage. For women with HA, this means ferritin may look deceptively low or “dysregulated,” not only from under-eating but also from stress-driven hepcidin activity.
Complicating this further, high cortisol also suppresses hypothalamic signaling, which lowers estrogen and progesterone. (13) As noted earlier, these reproductive hormones play an important role in nutrient absorption and their suppression can lead to significantly reduced mineral absorption (i.e. iron). (15) The combined effect of stress hormones up + reproductive hormones down creates the perfect storm for disrupted ferritin, folate, and iron balance.
Why Restoring Your Cycle Helps
Recovering from HA and restoring regular menstrual cycles supports ferritin levels in several ways. First, it signals that the body is once again receiving enough energy and nutrients to maintain reproductive function. (1) Increasing food intake sufficiently will often mean improved overall intake of iron-rich foods (like red meat, poultry, legumes, and dark leafy greens) along with cofactors such as vitamin C, folate, and vitamin B12 that aid iron absorption and red blood cell formation. With dietary restriction lifted, the body has a much greater capacity to build and maintain iron stores. Cycle restoration also helps normalize gut function, which is often impaired in states of undernutrition and chronic stress. (6,16) Through adequate nutrition and variety in food intake, slowly the gut microbiome can rebalance and this enhances nutrient absorption, including iron and folate. Finally, the return of healthy reproductive hormones—especially estrogen—further supports iron metabolism. Estrogen has beneficial effects on the gut and helps regulate hepcidin, the hormone that controls iron absorption. (2,10) Lower cortisol levels with recovery also reduce inflammation-driven hepcidin elevation, making iron more available for storage in ferritin. (2)
In short, restoring your cycle not only results in hormonal balance, but also creates the optimal environment for absorbing, utilizing, and storing iron effectively.
Feeling confused by low ferritin, iron, or folate levels during recovery?
If your labs show deficiencies even though you’re not bleeding, you’re not alone. In hypothalamic amenorrhea, low iron markers aren’t just about what you eat — they’re a reflection of your body’s energy and hormone balance. Without enough estrogen and fuel, your body can’t properly absorb, store, or use iron.
Through our 1:1 coaching and group coaching programs at The HA Society, we help you understand what your labs are really saying, restore balance to your hormones, and rebuild the energy your body needs to regulate iron and bring your cycle back naturally.
Recovery isn’t just about restarting your period — it’s about creating a body that feels nourished, energized, and truly healthy from the inside out.
Keep Reading:
What is Hypothalamic Amenorrhea?
Why Ferritin Levels Can Be High in Hypothalamic Amenorrhea (Even When Iron Is Low)
What Labs to Request if You Suspect Functional Hypothalamic Amenorrhea (HA)
References:
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2) Ryterska, K., Kordek, A., & Załęska, P. (2021). Has menstruation disappeared? Functional hypothalamic amenorrhea—What is this story about? Nutrients, 13(8), 2827. https://doi.org/10.3390/nu13082827
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