Introduction: The Chemistry of Your Feelings
Anxiety, depression, or that restless “tired but wired” feeling are never just in your head. They are signals that your internal chemistry needs attention. Hormones, neurotransmitters, and a handful of often‑overlooked nutrients run the show behind the scenes. When they aren’t supportive of your chemistry, mental health challenges can follow.
Conventional mental‑health care can miss these intricate connections, focusing often on talk therapy or medication to influence downstream chemistry changes alone. Functional medicine attempts to step back, look upstream, and asks: what is pushing the chemistry out of balance for this unique person…male or female, young or older?
Today we will map those drivers and lay out practical, evidence‑based corrections you can start diving into right away.
Stress Hormones: Cortisol and the HPA Axis
The hypothalamic‑pituitary‑adrenal (HPA) axis is your built-in alert system. It’s the master control center of many functional processes throughout the entire body.
Short-term cortisol bursts help you handle deadlines or dodge danger, whether actual or perceived. However, long-term increases in cortisol keep the brain in threat mode, dampens serotonin production, and even shrinks the hippocampus, a brain region tied to memory and mental health.
One of the biggest challenges I see in modern health with my patients is how we misunderstand stress. I often hear them say, “But I’m not stressed,” even as they describe their packed schedules, poor sleep quality, skipped meals, or intense workout regimens.
The truth is, stress isn’t just a state of obvious emotional overwhelm. It’s anything that increases demand on your body’s systems, what I call “hidden stressors”. And often, your hormones and nutrient stores are the ones waving the first red flags, long before your mind catches up.
High cortisol also robs magnesium and zinc, slows the conversion of active thyroid hormone, and shunts supplies needed to make sex hormones. The result can be a triple‑hit: anxious energy, low mood, and hormonal imbalance.
For a deeper dive, see my post “Understanding HPA Axis Dysfunction: Looking Beyond “Adrenal Fatigue”.
Thyroid Hormones: The Energy Spark Plugs for the Brain
Thyroid hormones tell every cell how fast to make energy. When levels dip, whether from autoimmune Hashimoto’s, iodine deficiency, or HPA axis interference, brain cells run on less power. Symptoms can feel like classic depression: low motivation, heavy fatigue, and slowed thinking.
Low thyroid function in both men and women can go unnoticed for years because a borderline thyroid panel often looks “normal.” A full workup includes TSH, free T4, free T3, reverse T3, and thyroid antibodies. But all too often, just a TSH is run, which catches the masses, but less the nuance. Optimizing conversion of T4 to active T3 frequently lifts mood before an antidepressant is even considered.
This is a perfect example of treating depression with a single medication that forces neurotransmitter activity, without addressing the root cause, which could be something like low thyroid function.
Sex Hormones Across the Lifespan
Estrogen and Progesterone in Women
Estrogen boosts serotonin and dopamine signaling, supporting calm focus and positive outlook. As levels rise mid‑cycle many women notice mental clarity and confidence. When estrogen dips pre‑menstrually or during perimenopause, mental health can suffer, and brain fog creeps in. (PubMed)
Progesterone, meanwhile, converts into allopregnanolone, a neurosteroid that calms the GABA receptor. Low progesterone relative to estrogen…often called estrogen dominance…shows up as irritability, anxious rumination, and sleep difficulty. Addressing gut health, stress load, and nutrient cofactors like vitamin B6 can help restore this delicate dance.
Testosterone and Estrogen in Men
Optimal testosterone supports motivation, emotional resilience, and neuroplasticity. Chronic stress, excess alcohol, visceral fat, and poor sleep all suppress testosterone, while insulin resistance and body fat converts testosterone toward active estrogen via aromatase.
Routine labs should measure total and free testosterone, estradiol, fasting insulin, sex hormone binding globulin (SHBG) and even salivary cortisol to reveal where the metabolic bottleneck starts.
Nutrients That Support Mental Health
Magnesium: Nature’s “Chill Pill”
Magnesium basically bathes our nerve cells and is incredibly important in brain and nervous system function. It controls calcium flow in nerve cells and co‑activates enzymes that make serotonin and melatonin.
The fact is that low intake is widespread due to soil depletion and processed food in the standard American diet. In fact, about half of US adults don’t consume enough magnesium to meet minimum requirements, let alone enough when demand is increased!
A 2023 meta‑analysis of randomized controlled trials found that targeted magnesium glycinate or citrate lowered depression scores in as little as six weeks.
Aim for at least 400 mg daily from spinach, pumpkin seeds, black beans, and yes, dark chocolate (at least 70%+). If you’re supplementing, splitting doses with meals can help avoid loose bowel movements and pair with a little vitamin B6 for better uptake.
The B‑Complex Vitamins: The Architects
Vitamins B6, folate (B9), and B12 donate their methyl groups to help create serotonin, dopamine, GABA, and norepinephrine. The rest of the B vitamins play important roles in energy production as well.
There is a wide variety of genetic variation in the population that concerns the ways they are able to absorb or convert B vitamins to their active, beneficial forms. For example, people with MTHFR or COMT gene variants burn through these vitamins faster, particularly under stress.
A 2019 systematic review found that B‑complex supplementation improved perceived stress and borderline depressive symptoms, especially in individuals with poor baseline status.
Food sources include leafy greens, pastured eggs, grass‑fed meat, and lentils. Vegans, older adults, and anyone on acid‑blocking medication should monitor B12 closely.
Omega‑3 Fatty Acids: Anti‑Inflammatory Powerhouses
EPA and DHA in fish oil make up brain‑cell membranes and lessen inflammation that can depress mood. An umbrella meta‑analysis of 22 studies concluded that omega‑3 supplementation…particularly formulas higher in EPA…exerts a small but significant improvement in depressive symptoms.
Shoot for two palm‑size servings of cold‑water fish weekly. If that is unrealistic, a distilled fish‑oil or algae‑oil supplement supplying 1-2 g EPA + DHA combined can be a helpful baseline.
Vitamin D: Sunshine in a Capsule
Vitamin D regulates more than 2,000 genes, including those that oversee serotonin creation and our immune response. An 18‑trial meta‑analysis in 2023 showed that vitamin D supplementation outperformed placebo in reducing depressive scores, with the greatest benefit in adults who started out deficient.
Check a 25‑OH D blood level; 40–60 ng/mL is a practical target, sometimes higher depending on the person and their needs. Combining vitamin D supplements with magnesium and vitamin K2 can help increase their safety and utility.
Zinc: The Synaptic Gatekeeper
Zinc influences both GABA and glutamate receptors, balancing excitatory and calming signals. Systematic review data suggest zinc supplementation can ease anxiety, and deficiency is linked with treatment‑resistant depression.
Food sources include oysters, grass‑fed beef, pumpkin seeds. Pair zinc with copper monitoring for long‑term use because taking too much or long term zinc competes with the absorption of copper, another important micronutrient for brain and nervous system function.
The Gut‑Brain Connection: Absorption, Inflammation, and Mental Health
Your gut microbiome ferments fiber into short‑chain fatty acids (literally turn carbs into fats!) that nourish intestinal cells and affect neurochemicals like GABA. An imbalance microbiome (dysbiosis) or intestinal permeability (leaky gut) can spark low‑grade inflammation that can affect the brain.
Practical steps to support gut health include eating a diversity of colorful plants, targeted probiotics (look for Lactobacillus rhamnosus GG and Bifidobacterium longum 1714), and limiting ultra‑processed seed oils that feed inflammatory bacteria.
Twelve Hidden Stressors That Drain Hormones and Nutrients
- Blood‑sugar peaks and crashes from refined carbs
- Blue‑light screens within two hours of bed
- High‑intensity exercise with little recovery
- Skipping protein at breakfast
- Reheated seed‑oil takeout
- Hidden gut infections (H. pylori, candida, parasites)
- Household mold or mycotoxins
- Low‑grade food sensitivities (gluten, dairy)
- Undiagnosed sleep apnea
- Coffee or energy drinks after noon
- Chronic self‑criticism and rumination
- Mouth‑breathing or shallow chest breathing
Each item nudges cortisol higher, strips magnesium and B vitamins, and stalls thyroid conversion. Check my article “Stress: 12 Hidden Sources that May Be Impacting Your Health” for a deeper dive.
Mental Health & Life‑Stage Considerations
Adolescence
Rapid brain growth demands extra omega‑3s, zinc, iron, and B vitamins. Add the hormonal surge of puberty and social stressors, and mood can swing wildly. Emphasize balanced blood sugar, screen‑time boundaries, and lab checks less or highly active.
Pregnancy and Post‑Partum
Iron, DHA, choline, and iodine demands tend to skyrocket, while estrogen and progesterone climb, then plummet after delivery. Insufficient DHA or choline correlates with higher post‑partum depression risk. Work with a practitioner to personalize prenatal supplementation and track thyroid antibodies.
Perimenopause and Menopause
Estrogen drop‑offs change serotonin dynamics and impair magnesium retention. Hot flashes, insomnia, and mood lability often respond to magnesium, B6, omega‑3s, mindful strength training. When appropriate, bioidentical hormone therapy under supervision can be life-changing for some.
Andropause in Men
Free testosterone begins declining around age 35, accelerated by stress and insulin resistance. Resistance training, optimizing sleep, and ensuring adequate zinc, magnesium, and vitamin D often raise testosterone naturally. If levels stay low, evaluate sleep apnea and discuss bioidentical testosterone replacement.
Functional Testing: Turning Data into Direction
A combination of both conventional labs and function medicine labs can strategically guide the best treatment combination that can help support mental health from the inside out.
- Blood chemistry with insulin, hs‑CRP (inflammation/heart health), homocysteine, and nutrient markers
- Salivary or dried‑urine (such as the DUTCH test) cortisol curve for HPA Axis mapping
- Full thyroid panel (TSH, free T4, free T3, reverse T3, antibodies)
- Sex hormones with binding globulins and free fractions
- Comprehensive stool analysis or GI‑MAP for dysbiosis and leaky gut indicators
Lab data helps reveal whether mental health issues stem from nutrient gaps, hormone bottlenecks, gut inflammation, or all three. Testing also prevents the guess‑and‑stress cycle of random supplements.
Action Plan: Putting Science into Practice
- Build a Colorful Plate: Half vegetables, one‑quarter quality protein, one‑quarter smart carbs like quinoa or sweet potato, topped with olive oil or avocado.
- Anchor the Day: Morning sunlight within 30 minutes of waking, five‑minute box breathing before emails, and a 10‑minute evening stretch sequence calm the HPA axis.
- Supplement with Purpose: Typical starting stack (verify labs first):
- Magnesium glycinate 200–400 mg at night
- Methylated B‑complex with 400 mcg folate and 50 mcg B12
- Fish‑oil concentrate with 1.5 g EPA + DHA combined
- Vitamin D3/K2 to reach serum 40–60 ng/mL
- Zinc glycinate 15 mg with dinner (cycle if using long term and consider copper monitoring)
- Sleep Hygiene: Aim for 7–9 hours in a dark, cool room. Support melatonin production with a screen curfew and magnesium.
- Train Smart: Three resistance sessions per week plus daily walking improve insulin sensitivity and testosterone, curb cortisol, and deliver a steady mood boost.
Conclusion: Your Mental Health Is Malleable
Science confirms what many clients intuitively sense: Mood isn’t just mental…it’s metabolic and functional, too. When you give your brain and nervous system the raw materials they need to thrive (magnesium, B vitamins, omega‑3s, vitamin D, and zinc) and when you calm excess cortisol while optimizing thyroid and sex hormones, you create the biochemical soil where stable emotions can grow.
Ready for a personalized deep dive? Book your FREE Health Clarity Consult today. We can map your nutrient status, hormone patterns, and try to identify hidden stressors to craft a plan that supports calm energy and sharp focus…whatever your gender or life stage.
(For educational purposes only. Always consult your healthcare provider before changing medications or starting new supplements.)
About the Author
Kenny Mittelstadt is an acupuncturist and functional health practitioner based in San Antonio, Texas. He is trained through the Institute for Functional Medicine and received both of his doctorate degrees with highest honors from Southern California University of Health Sciences. He focuses on empowering patients through creating opportunities for integrated understanding and personalized root-cause healing - starting with gut health and growing beyond!