Athletes are a unique clinical population. They live in a state of intentional, repeated physiological stress, and are often highly disciplined, goal-oriented, and skilled at pushing through discomfort in pursuit of performance. When symptoms arise, they are frequently minimized, normalized, or attributed to fueling errors rather than prompting the deeper functional question of why the body is struggling in the first place.

I know this pattern well because I lived it. Before becoming a functional practitioner, I was a highly driven elite athlete chasing my ski racing dreams at both the professional and collegiate level. I believed I was doing everything “right”, training hard, eating clean, and relentlessly pursuing performance. Subtle signs that my body was struggling were easy to dismiss at the time: years of gut dysfunction, poor sleep, loss of my menstrual cycle, and increasing food sensitivities. Like many athletes, I continued to ignore these signals and pushed through, unwilling to let anything interfere with my goals or training plan.

I now see this pattern repeated in my own clients. It reflects a common pattern in athletes where the demands they put on their body quietly compromise the body’s ability to recover, adapt, and function. In practice, I often use a stress bucket analogy to illustrate this dynamic. Rather than continually bailing water out faster to keep up with the load, getting the best clinical outcomes with these clients requires an understanding of what is filling the bucket in the first place. When working with athlete clients, we still want to address the foundational pieces—starting with the gut, rebalancing blood sugar, etc.—but there may be additional contributors to the bucket overflow in high-performing athletes.

Here there are five key considerations:

Key Consideration #1: The Metabolic Mask

Athletes possess a unique physiological “buffer.” High levels of cardiovascular fitness and lean muscle mass can temporarily mask underlying metabolic dysfunction that may be bubbling under the surface [1]. As a result, early signs of imbalance, such as blood sugar dysregulation, are often overlooked or dismissed due to a strong perception of health and fitness.

It is not uncommon for athletes to rely on a diet that resembles the Standard American Diet (SAD), including high intake of refined carbohydrates, sugars, and ultra-processed training foods. In the short term, higher energy expenditure and improved insulin sensitivity can offset the consequences of these choices. But what happens long term if habits are not changed?

I recently worked with a retired collegiate athlete who was young, fit, and only a few years removed from competitive sport. Routine blood work revealed blood sugar markers in the pre-diabetic range, which came as a genuine surprise to him. As a former high-level athlete, he admitted he had never needed to think much about his eating habits, he could “get away with it.” As his training load decreased after retirement, however, his physiology could no longer compensate in the same way.

While increased levels of physical activity can have many metabolic benefits, I frequently see athletes with early signs of blood sugar dysregulation such as evening carbohydrate cravings, nighttime awakenings, and difficulty maintaining stable energy throughout the day. These signs can serve as early indicators that training load, fueling strategies, and recovery capacity are no longer aligned. This is where lab data becomes a powerful tool to both validate what the body is signaling, but also to motivate meaningful behavior change when the athlete feels largely symptom free.

Key Consideration #2: Gut Integrity, Microbiome Balance and GI Distress

The gut is particularly sensitive to training load and intensity. At low to moderate intensities, exercise can be extremely beneficial for gut health. It can improve barrier integrity, increase microbiome diversity, and enhance the production of short-chain fatty acids (SCFAs). Exercise also supports nutrient and electrolyte absorption and assimilation and the clearance of toxic metabolic products [2]. However, there is a tipping point. As training volume and intensity increase, exercise-related stress can begin to compromise intestinal barrier function and alter microbial balance, including shifts in the Firmicutes:Bacteroidetes ratio [3]. Too much of a good thing can be harmful.

More acutely, the prevalence of GI issues in endurance sports is known. It is estimated that 30–90% of distance runners experience exercise-induced GI issues, including urgency, diarrhea, abdominal cramping, nausea, or vomiting. These symptoms are most often driven by physiological stressors during higher intensity training or competition including reduced blood flow to the gut, mechanical stress, dehydration, and fueling strategies [4]. It is possible then that repeated episodes of exercise-induced GI distress, layered on top of high training load and under recovery, may contribute over time to increased gut vulnerability and should not be dismissed as “just part of the sport” as they often are.

When working with high-performing athletes, it is essential to consider the increased propensity for intestinal permeability, dysbiosis, and GI inflammation. As we know, compromised gut barrier function can further drive systemic inflammation and food sensitivities. Addressing the health of the gut through stool testing paired with MRT food sensitivity testing can significantly reduce the immune and inflammatory burden and improve clinical outcomes with these clients.

I worked with a woman who struggled with exercise-induced GI issues. She was training for her first 100-mile running race and was experiencing extreme urgency during her training and races. When we dug deeper with a GI Map, we saw intestinal permeability with low Akkermansia muciniphilia, low butyrate/SCFA production with low levels of Faecalibacterium prausnitzii, Rosburia, and Firmicutes phyla. She also had high levels of a few inflammatory and autoimmune-related bacteria such as Citrobacter spp., which is known to drive intestinal inflammatory activity, and elevated levels of steatocrit indicating undigested fat in her stool. A few weeks into supporting her gut and digestive function, she noted that her urgency had improved significantly. Midway into her protocol she reported that she did a 20k training race with zero emergency bathroom breaks. This is an example of just how powerful supporting the gut can be with athletes.

Consideration #3: Systemic Inflammation & Oxidative Stress

Systemic inflammation is an important consideration when working with athletes, particularly when we step back and look at what’s driving it and its full-body impact. Training itself is a controlled form of injury, and the inflammatory response that follows is not only expected but necessary for tissue repair, growth, and adaptation. The challenge arises when recovery capacity cannot keep up with cumulative training stress. Very quickly, this can put the body into overdrive.

Unresolved chronic inflammation does more than impair athletic performance, it places stress on multiple physiological systems, the immune system, and overall health [5]. When an athlete is overtraining or under recovering, there is sustained pro-inflammatory signaling alongside increased production of reactive oxygen species (ROS). While ROS plays an important role in training adaptation, problems arise when oxidative load exceeds the body’s antioxidant defenses and recovery resources. At that point, oxidative stress develops, contributing to cellular and tissue damage. What begins as a localized training response can evolve into pathological changes across multiple tissues and organ systems, including skeletal muscle, the hypothalamus, the heart, and the liver [6].

In practice, systemic inflammation and oxidative stress rarely present as a single abnormal lab value. Instead, look for signs and symptoms and assess for patterns. Athletes may report poor or delayed recovery, exaggerated delayed onset muscle soreness (DOMS), recurring injuries, persistent fatigue, declining training tolerance, or a plateau in training. Dialing back training volume and intensity is often a necessary step to reduce the inflammatory burden, stabilize the stress bucket, and restore the body’s capacity to adapt and recover. Regarding blood chemistry, inflammatory biomarkers such as CRP and hsCRP may appear normal or only mildly elevated, so assessing patterns is key.

When building protocol recommendations, I emphasize an anti-inflammatory diet rich in antioxidants to support the oxidative stress and inflammatory response. For supplements, I often consider high-dose omega-3 fatty acids, specialized pro-resolving mediators (SPMs), and additional antioxidant support including glutathione or NAC, CoQ10, and sulforaphane, depending on the athlete’s presentation and tolerance. Lifestyle factors are equally critical—sleep hygiene, intentional recovery days, and nervous system regulation are foundational. Athletes often train hard by default; learning to recover with the same intention is frequently the missing piece.

Consideration #4: Nutrients Beyond Calories

When working with athletes, nutrient status deserves careful attention. Not only are their caloric needs higher, but their nutrient demands, turnover, and losses are significantly higher as well [7]. Training increases the utilization and excretion of key nutrients including iron, magnesium, zinc, electrolytes, several B vitamins, and vitamin D.

A common pattern in this population is a tendency toward DIY supplementation. Athletes are often motivated, data-driven, and looking for an edge in performance or recovery, which means they may be taking multiple supplements they believe they “should” need, often without targeted testing or a clear understanding of absorption, interactions, or root cause. This can lead to imbalances, missed diagnoses, or frustration when symptoms persist despite doing “all the right things.”

When addressing nutrient deficiencies in athletes, the most important step is to ask the deeper question of why. Is the issue driven by impaired digestion or absorption? Ongoing pathogen burden? Increased training demand? Dietary insufficiency? Or a combination of these factors? In high-performing athletes, nutrient deficiencies are rarely random, and supplementation alone often fails to resolve symptoms if upstream drivers are not addressed.

I worked with an ultra runner who came to me taking iron for persistent fatigue and low ferritin identified on blood work with her primary care provider. While iron deficiency is common in female endurance athletes [8], deeper investigation revealed elevated H. pylori, multiple parasitic infections, and deficiencies in several B vitamins and other nutrients essential for stomach acid production and iron absorption. In her case, iron was not the primary problem. Impaired digestion, reduced absorption capacity, and parasites stealing her iron were driving the deficiency.

Consideration #5: Hormone Impacts & HPA Axis Dysfunction

There are many contributing factors to hypothalamus-pituitary-adrenal (HPA) axis dysfunction and hormone imbalance, but in athletes, a major one to consider is the impact of training. Training is, by definition, stress. When appropriately dosed and paired with adequate recovery, this stress drives positive adaptation, improved performance, and overall health. Trouble arises when training stress becomes chronic, shifting the stress response from adaptive to dysregulated.

The HPA axis coordinates the body’s response to stress and plays a critical role in blood sugar regulation, inflammation control, immune signaling, sleep, and recovery. Under normal conditions, moderate to intense exercise produces a predictable and healthy adaptive activation of the HPA axis. Cortisol and adrenocorticotropic hormone (ACTH) rise in response to training stress and return back to baseline within hours of exercise.

In contrast, hormonal patterns associated with chronic overtraining tell a different story. Rather than seeing an appropriate rise in cortisol and ACTH from exercise, overtrained athletes often exhibit blunted cortisol and reduced anabolic hormone responses [9]. Essentially, the HPA axis becomes less responsive to continued exposure to stress. This loss in adaptive capacity reflects increased allostatic load—the cumulative “wear and tear” of chronic stress—and helps explain why performance decreases, fatigue deepens, and recovery slows despite continued training.

Importantly, the effects of chronic HPA-axis dysfunction extend beyond cortisol. Downstream impacts can affect nearly every organ and system of the body including the gut, brain, thyroid, sex hormones, and immune system. Endurance athletes may be particularly susceptible, as prolonged aerobic exercise promotes sustained sympathetic (“fight or flight”) dominance, indicated by elevated cortisol levels [10][11]. Over time, this can impair the body’s ability to shift efficiently between stress and recovery states.

While athletes may be more prone to hormone imbalance and HPA axis dysfunction due to the added stress of overtraining and under-recovery, the clinical approach to supporting them is the same. Hormone imbalance must be approached through addressing the foundations of gut and microbiome health, blood sugar regulation, inflammation, hormone metabolism and detoxification, balanced nutrients and hydration, stress, and sleep. I start here before diving into hormone testing.

One client, a recreational mountain athlete, came to me after working with various other functional practitioners without meaningful improvement in her primary concerns: deep fatigue, slow recovery from training, waking in the middle of the night, and heavy painful periods with midcycle bleeding. She had already tried adrenal support, liver support, and supplementing nutrient deficiencies. She was frustrated and overwhelmed. Instead of chasing symptoms, we focused on the foundations of hormone imbalance and honoring the healing priorities of the body. Within a few weeks she was sleeping through the night and waking with more energy. After about two months into her protocol, she reported having the easiest menstrual cycle she had experienced in over a year, with no midcycle bleeding.

This case illustrates the importance of focusing on the foundational drivers of hormone imbalance rather than the symptoms themselves.