How Your Body Actually Makes Energy (And Why It Stops)
This is part 3 of a 4-part series on fatigue. If this is your first time here, start with part 1.
Energy and Fatigue Series · Part 3 of 4
Part 1: Why you’re always tired · Part 2: Why nothing is working · Part 3: How energy is produced · Part 4: What your body needs
The short answer: your body makes energy inside structures called mitochondria, using nutrients and oxygen. When chronic stress keeps cortisol elevated, it impairs that process directly. Digestion slows, nutrients stop absorbing properly, and cellular energy production drops. Persistent fatigue is not a motivation problem. It is the body running out of the conditions it needs to make energy reliably.
You have tried the sleep. You have tried the supplements. You understand now that the nervous system is running the show and that the usual approaches do not reach the root.
But there is still a question worth answering.
What is actually happening in your body when energy breaks down? Not the symptoms. The mechanism. Because when you understand this part, everything else starts to make a different kind of sense.
Where energy actually comes from
Every cell in your body runs on a molecule called ATP. It is made inside mitochondria, using nutrients and oxygen. When the conditions for that process are disrupted, energy drops regardless of how much rest you get.
Think of mitochondria as the power stations inside your cells. They take in fuel, mainly glucose and fats, and convert it into a form the body can actually use. That form is ATP.
ATP powers everything. Your heartbeat. Your digestion. Your ability to think clearly. Every biological process in your body is drawing from that same supply.
The catch is that making ATP requires specific conditions. The right nutrients. The right enzymes. The right environment. When those conditions are disrupted, production slows. And that slowdown is what you feel as fatigue.
This is why persistent fatigue does not respond to rest alone. You can sleep eight hours inside a body that is not producing energy efficiently and still wake up depleted. Because the problem is upstream from the sleep.
What stress is actually doing to your energy
Cortisol is useful in short bursts. But when it stays elevated over months or years, it directly impairs the mitochondria. It reduces the activity of the enzymes that make ATP. It disrupts the hormonal environment your cells need to access fuel. And it suppresses the digestive function required to absorb the nutrients your mitochondria depend on.
Cortisol is your body's primary stress hormone. In the short term it is a good thing. It sharpens focus, mobilizes fuel, and helps you respond to demands. That is what it is designed to do.
The problem is what happens when your system has been running that response for a long time.
Research has shown that chronically elevated cortisol reduces the activity of key enzymes in the energy production chain, impairs the structural integrity of mitochondria themselves, and suppresses thyroid function and sex hormone production, all of which affect how efficiently your cells can produce and use ATP. [1]
Your body is not failing to make energy. It is choosing survival over efficiency. And that is a completely rational response to a system that has been reading threat for too long.
“Your body is not failing at energy production. It is running a stress response at the expense of it.”
Why your supplements may not be working
Mitochondria need specific micronutrients to function: B vitamins, magnesium, iron, and coenzyme Q10 among others. Chronic stress depletes these nutrients and, critically, suppresses the digestive processes that allow them to absorb. You can be taking the right things and still not absorbing them effectively.
Your mitochondria cannot make energy without raw materials. And several of those raw materials are nutrients that chronic stress actively depletes.
B VITAMINS
Essential at every stage of ATP production. Rapidly depleted by chronic cortisol. Poorly absorbed when gut function is suppressed.MAGNESIUM
Required for ATP synthesis and over 300 other enzymatic reactions. Excreted in higher quantities under stress.IRON
Carries oxygen to your cells. Chronic inflammation from stress impairs how the body uses it, even when levels look normal on labs.COENZYME Q10
A key component of the final stage of energy production. Declines with age and with chronic stress.
The deeper problem is that chronic stress suppresses the very digestive processes that allow these nutrients to absorb in the first place. Research has documented how sustained stress depletes key micronutrients through multiple pathways simultaneously: increased excretion, reduced intake, and impaired absorption due to gut suppression. [2]
That is why so many women do everything right with supplementation and still feel no different. It is not the protocol. It is the bucket with the hole in the bottom that we talked about in part 2.
Why perimenopause makes all of this louder
Estrogen plays a direct protective role in mitochondrial health. As it declines in perimenopause, the mitochondria become more vulnerable to stress-induced damage. At the same time, declining progesterone reduces the nervous system's natural buffer against stress reactivity. The result is that fatigue which was manageable in earlier years becomes increasingly hard to push through.
Many women describe a shift in their 40s where fatigue stops being something they can manage and becomes something they have to work around. The life has not necessarily become more demanding. But the body's capacity has shifted.
Estrogen supports the process by which the body makes new mitochondria and protects existing ones from oxidative damage. Research has documented how estrogen decline accelerates mitochondrial dysfunction and reduces cellular energy capacity in ways that map directly onto perimenopausal fatigue. [3]
Progesterone has a calming effect on the nervous system through its conversion to a neurosteroid that supports the brain's primary inhibitory pathway. As progesterone declines, this natural dampening effect on stress reactivity diminishes. The nervous system becomes more easily triggered and slower to settle.
Nothing entirely new has gone wrong. Everything that was already under strain has simply become harder to carry.
What this means for you
Understanding the mechanism changes what makes sense to do about it.
If energy production is breaking down because of cortisol, suppressed absorption, and a nervous system that cannot fully restore, then working at the level of those conditions is what creates change.
That means the nervous system has to be the starting point. Not a meditation app as an add-on, but genuine nervous system support as the primary target. When the nervous system is no longer reading chronic threat, the cortisol drops, digestion restores, nutrients begin to absorb, and the mitochondria can finally do their job.
It also means that recovery is cumulative. The load built up over time, and rebuilding capacity takes time too. This is not a failure of the approach. It is how biology works.
Your body has not forgotten how to make energy. The capacity is still there. The conditions just have not been right.
“When the body is given what it needs, it already knows what to do.”
That is not a motivational statement. It is a physiological one.
Next week is the final part of this series. We are going to look at what it actually means to create those conditions, and what your body needs in order for energy to become something you can rely on rather than something you have to force.
Questions I hear often
Why am I so tired even when I eat well and sleep enough?
Because eating and sleeping happen inside a nervous system. If that system is running a chronic stress response, cortisol is impairing your mitochondria, your gut is not absorbing properly, and sleep is not restoring the way it should. The problem is not the inputs. It is the physiological state those inputs are landing in.
Can stress actually damage my mitochondria?
Yes. Chronically elevated cortisol reduces the activity of key energy-producing enzymes and impairs the structural integrity of mitochondria. The good news is that this is reversible with appropriate support. But it requires addressing the chronic stress response, not just managing its symptoms.
Why is my fatigue so much worse in perimenopause?
Estrogen protects mitochondrial function and progesterone buffers the stress response. As both decline, the mitochondria become more vulnerable and the nervous system becomes more reactive. Any chronic stress load that was already present gets amplified significantly. It is not that everything has gone wrong. It is that the body's cushioning has thinned.
Why are my supplements not helping?
Most likely because the gut function required to absorb them has been suppressed by chronic stress. The right nutrients in a compromised absorption environment will not land the way they should. Supporting absorptive capacity is the prerequisite, not the afterthought.
This is part 3 of 4
Part 1: Why am I always tired, even when I sleep enough?
Part 2: Why rest, supplements, and self-care are not fixing your fatigue
Part 3: How your body actually makes energy and why it stops (you are here)
Part 4: What your body actually needs to feel energized again (next week)
REFERENCES
1. Bhatt D, Singh R, et al. Cortisol, mitochondrial function, and cellular energy production. Frontiers in Physiology. 2024. [Chronic cortisol elevation, enzyme activity in the electron transport chain, and mitochondrial fragmentation.]
2. Lopresti AL. The effects of psychological and environmental stress on micronutrient concentrations in the body: a review of the evidence. Advances in Nutrition. 2020;11(1):103-112. PMC7442351.
3. Singh R, et al. Perimenopausal fatigue mechanisms: oestrogen, mitochondrial biogenesis, and HPA axis reactivity. Endocrine Reviews. 2025.
If this is landing for you and you are ready to understand what your body actually needs, that is the work we do at Santosha Wellness. Not managing fatigue. Restoring the conditions that make energy sustainable.
What if fatigue is not a fixed state, but a signal that the system is ready to shift?
Part 4 is next week. If you want to talk about what this looks like for you specifically in the meantime, the link below is where to start.
