The Best Workouts And Exercise for Leaky Gut + 15 Strategies to Prevent It

Written By


Expert Reviewed By

Dr. Lauryn Lax, OTD, MS

Dr. Lauryn, OTD, MS is a doctor of occupational therapy, clinical nutritionists and functional medicine expert with 25 years of clinical and personal experience in healing from complex chronic health issues and helping others do the same.

Exercise For Leaky Gut - Woman About To Start To Run

It’s been estimated that upwards of 90% of athletes—especially endurance athletes— have a functional gut disorder (1, 2).

Exercise for leaky gut, like sleep, green things and water, does a body good…until you go overboard with too much exercise. Too much exercise and training can further promote gut problems like leaky gut, SIBO, IBS, abdominal pain, bloating and constipation and beyond.

So what are the best types of workouts and best exercise for optimal gut health?

Read on for all your need to know on  the best science-backed exercise and nutrition and lifestyle strategies for both treating and preventing leaky gut during workouts.

Cons & Pros: Effects of Exercise on Gut Health

Exercise For Leaky Gut - Woman Who Is Running

Constipation, bloating or bad digestion got you down, despite doing all the things to be healthy (like working out and eating right)?

Research finds there is a strong connection in athletes who experience GI symptoms and having a history of GI symptoms throughout their life (3, 4). In other words, if you have a history of struggling with constipation and bloating, exercise may exacerbate your symptoms more—especially if you don’t follow the strategies and hacks described below in this article.

That said, exercise can have beneficial effects on gut health as well. Let’s briefly discuss the cons and the pros of exercise on gut health. 

Cons: Effects of Exercise on Gut Health

Exercise On Gut Health - Woman Doing High Intensity All Out Exercise

  1. Exercise—particularly acute aerobic exercise and intense all-out exercise (think CrossFit 7 days per week)—restricts blood flow to your gut. If you “go hard” every day, herein lies a problem (4): Constipation, bloating and irregular bowel habits. “Steady state” exercise (such as running, elliptical, spinning, cardio, a LONG met-con session) has been shown to reduce blood flow to the gut by 20% within just 10minutes, and by 80% after 1 hour of working out at 70% of maximal oxygen update (5).
  2. Increased carbs during exercise are associated with increased risks for nausea, gas and bloating. Exercise sometimes demands athletes intake higher amounts of carbs. While carbs can be great for enhnaced performance, higher intakes of carbs —especially if combined with extra sugars, artificial sweeteners and other artificial ingredients found in powders and shakes—may further exacerbate ill gut health (6).
  3. Strenuous exercise destroys the integrity of a healthy gut, leading to leaky gut and metabolic endotexemia. A major consequence of strenuous exercise (basically a hard workout) is “epithelial injury”—damage to your gut lining leading to increased intestinal permeability. Just 1 hour of running at 70% of your VO2max has been shown to perturb the tight junctions of your gut (7). Thus, frequently working out hard results in physical breaks for your gut epithelium and dysfunction of your tight‐junction regulatory proteins (8). Evidence suggests that an elevation in free radicals, inflammation and lipopolysaccharides (toxins from gut bacteria) occurs immediately after an intense bout of exercise (9).
  4. Too much exercise disrupts a healthy gut microbiome, leading to malabsorption and chronic gut problems. A big consequence of disruption to gut barrier integrity is also heightened “bacterial translocation” (ie. Disruption of balanced healthy gut bugs). Bacteria are abruptly moved from their home and thrown “onto the streets”—out of their element. As a result, they release bacterial endotoxins (likelipopolysaccharide) directly after endurance exercise (10, 11, 12). Without a healthy ecosystem, malabsorption of nutrients is a downstream effect (13).
  5. Overtraining alters hormone and immune balance. Simply put, a disrupted gut from strenuous exercise and overtraining equals a disrupted HPA Axis (brain-gut connection) (14), which effects hormone balance (cortisol, estrogens, testosterones and beyond) and a disrupted gut equals a disrupted immune system (considering that 70% of your immune system is actually housed in your gut.Normally, you have are two “protective” immune mechanisms that deal with increased gut bacteria translocation, leaky gut and inflammation. First: “anti‐endotoxin antibodies help destroy and clear of bacterial endotoxins, and, second: immune cells themselves fight (like firefighters) against pro‐inflammatory cytokine responses (ie, elevated Interleukin‐1β, TNFα and Interleukin‐6, Interleukin‐8, etc.). However strenuous, repetitive exercise (again, going “hard” day in and day out), reduces your natural ability to defend against systemic inflammation (15). 

Pros: Effects Exercise on Gut Health

Exercise On Gut Health - Woman Doing Exercise Happily

  1. Exercise improves gut motility and can prevent constipation. Sit all day and your bowels stay stagnant. Move and get flowing and voila, the golden poo is yours for the taking! (16, 17).
  2. Exercise promotes lymphatic drainage for daily cleansing. Your lymphatic system acts like the “Nile River” of your body—flushing toxins, undigested food particles, bacteria and pathogens out, while delivering nutrients to all organs and systems in your body. Exercise naturally gets your drains “flowing”, just like it aids in gut motility.
  3. Exercise enhances brain health for improved gut-brain function. Movement is medicine (18, 19). Exercise acts like a natural anti-anxiety, anti-depressant and mood and brain booster all in one. Considering that your gut is your “second brain” (containing over 500 million brain cells in it alone), when you enhance your brain health, you naturally enhance your gut health.
  4. Appropriate exercise inhibits unhealthy gut bacteria from overcrowding your system. Although too much exercise can be like poking a wasp nest for your gut microbiome, tons of research finds that healthy amounts of exercise actually foster a healthier gut ecosystem (shocker, right?). Moreover, body fat percentage, lean muscle mass and enhanced overall health is significantly correlated with healthier gut microbiota populations from regular exercise (20).
  5. Exercise encourages healthy eating and sleeping habits. Exercise goes hand in hand with the other pillars of health—eating “right” and getting enough sleep. For many folks, exercise is like the domino effect for building healthier habits into their lives in other areas (21, 22). For example, natural melatonin production is positively impacted by regular appropriate exercise (23), and hyperthermia (sweating) during exercise leads to increases in “deep” and quality sleep (24). As for food, a regular dose of exercise in our daily lives is related to both decreased snacking and sugar cravings (22). 

Best Workouts & Exercise for Leaky Gut

So, considering both the pros and the cons of exercise on the gut microbiome, what are the best workouts and types of exercise for leaky gut?

One word: Balance.

If there is any theme discovered from the “cons” of exercise on the gut, it is continual, repetitive and strenuous exercise does not do a gut biome good.

Additionally, “more exercise” is not necessarily better.

For that reason, a balanced fitness routine, combined with the proactive “gut health” strategies below can help both weekend warriors and athletes alike enhance their gut health and prevent the negative consequences of exercise on the gut.

“Balanced” workouts look differently for every individual.

For example, a “balanced” workout routine for an elite athlete, like Michael Phelps, actually looks like daily recovery—sleeping 8 hours every night, napping 2 to 3 hours each afternoon, taking 1 “active rest day” per week and pro-actively consuming upwards of 12,000 calories daily in order to support his 5 to 6 hours of training and 13 km that he  swims every day. Basically, Phelps goes to the opposite recovery extremes in order to balance out his extreme training schedule.

Similarly, for the cardio junkies out there (ie. a marathoner, tri-athlete or avid trail runner), a “balanced” workout routine for better gut health would also be found in the optimization exogenous recovery tactics (outlined below) to counter the gut damage seen most commonly in research.

Lastly, for a gym junkie or CrossFit enthusiast, a “balanced” workout routine may look like 3 days on of varied workouts (combining strength, endurance, flexibility and power movements) at a moderate intensity the majority of the time (70% or less versus 70-100% intensity), plus 1 day off—a recovery or active rest day, then repeating.

This variance in workouts, dynamic and daily lifestyle movements, at a moderate and low intensity effort, are perhaps the “best” for the gut biome. Combine formal exercise 5 to 6 days per week with daily activities like walking, hiking, yoga and simply an active lifestyle to foster a healthy gut ecosphere (25, 26, 27, 28).

Ultimately, as long as you are optimizing recovery and not driving your body into the ground, day in and day out, an athletic microbiome can make you a healthier person all around (29, 30)—including more gut diversity, enhanced short-chain fatty acids, a healthier leaner gut-muscle axis, and more balanced diet.

15 Leaky Gut Healing Strategies: Pre-Workout, During Exercise & Post-Workout

Exercise On Gut Health - Pre Workout Strategies, Water, Banana, Tape Measure, Notebook, Apple

Support your gut to optimize your fitness “gains” inside and out with these strategies for pre-workout, post-workout and in-competition and training feats. 

5 Pre-Workout Strategies to Prevent Gut Problems Before Exercise 

#1. Avoid Caffeine

Caffeine— both coffee and energy drinks—can provoke GI distress (31).  Caffeine, especially coffee, works like a natural laxative, activating contractions in the colon, your gallbladder and intestinal muscles, consequently making you need to poo. Caffeine also stimulates the hormone gastrin that helps propel food through the digestive tract and makes your colon more active. Although going #2 is encouraged, it prevents optimal exercise and training time if you get stuck in the loo. 

#2. Hydrate Before You Train

Dehydration exacerbates exercise‐associated gut problems. For example, a study of participants who sat in a sauna prior to cycling at 70% VO2Max found athletes experienced increased nausea, bloating and abdominal pain, compared to hydrated athletes (32). Aim to drink at least half your bodyweight in ounces daily and supplement with trace minerals for minerals lost via sweat and training (33). 

#3. Poo Before Activity

If possible, try to go #2 at least once in the day before engaging in exercise. Exercise stimulates bowels to move and groove. If you struggle with constipation, some of my favorite supports include:

#4. Eat Foods That Support Your Gut

We all know real food is good for us—meats and fish, fruits, vegetables, healthy fats, nuts and seeds. However, sometimes even “healthy” foods can trigger GI distress. Keep a food diary to identify what foods, if any, are bothersome to your gut. Also, avoid more than 10% of daily carb in the form of glucose solutions and artificial sweeteners (like Gatorade, Propel and other sports drinks with ingredients like Maltodextrin), as these can promote diarrhea.

#5. Dont Eat a Large Meal Before Training

Ideally allow 3 hours prior to any “intense” training or competition to prevent blood flow restriction to the gut (34). 

5 Strategies to Minimize Gut Problems During Exercise 

#1. Breathe Properly

Exercise On Gut Health - Woman Properly Breathing

Upper GI issues in athletes are exacerbated by poor oxygen uptake (35). Without proper oxygenation, inflammation increases and gut ischemia happens (ie. Decreased blood flow to the gut). Aim to utilize nasal breathing as much as possible (for inhalation at the very least) with deep complete breathes, and breathe with your diaphragm and belly, as opposed to your chest—your full rib cage should expand. 

#2. Consume Easy-to-Digest Carbohydrates & Proteins During Exercise

For exercise longer than 2 hours, research shows ingesting 15 g of carbohydrate along with water during workouts can be beneficial for protecting against exercise‐induced gut disturbances. Whey and protein powders have also shown similar benefits as on protecting the gut lining, however GI symptoms were also much higher, suggesting possible problems with tolerating protein during exercise (36). On the contrary, goos, carb gels and other transportable carbs (bars) don’t seem to digest as well and may exacerbate gut symptoms (37).

#3. Gradually Enhance Training

Don’t bite off more than you can chew. Gradual increases in exercise duration, intensity, efforts and weights/resistance leads to more productive shifts in the gut versus all-out-stress (this is why Michael Phelps is Michael Phelps—years of practice and increases in his training threshold and endurance) (38, 39).

#4. Flood Your Gut with Support During Training

It has been shown that 60 minutes of vigorous endurance training (especially cardio activities like running, cycling, etc.) and/or at 70% of the maximum work capacity leads to leaky gut symptoms, decreased motility (constipation) or IBS, and increased systemic inflammation. While there is absolutely no need to “hit a wall” during training, researchers wanted to know: Is there an “exercise intensity” threshold capable of avoiding leaky gut? (40) It appears there is—if you support your gut with all the tools in your tool belt you may be able to “go harder” than other athletes. Gut loving support tools include things like: avoiding extremely hot temps, hydration, training aligned with your circadian rhythms (sleep-wake cycles) and training more often in the low-to-moderate exercise threshold (30-70% intensity, versus 70%+ intensity). 

#5. Listen to Your Body

If you follow a workout routine or program, and you really aren’t “feeling” a particular workout that day, resting or supplementing an alternate workout may do both your fitness and gut microbiome better in the long run. Increased intestinal permeability results when we don’t listen to our bodies and push the intensity day in, day out. Although “no pain, no gain” or “work hard, play hard” may be mantras that continually play into your head, research does not support this methodology for enhancing your performance and health. (In fact, chronic disease and autoimmunity goes hand-in-hand with high intensity exercisers who continually push themselves) (41). No, you do not have to sit on a couch and eat Ben & Jerry to “rest”, however flexibility with your routine and alternative training routines is encouraged. After all, if you’re one of the 1 in 5  people who actually follows a training-style workout routine regularly, rest is part of improving outcomes. 

5 Post-Workout Strategies to Recover Your Gut Health After Exercise 

#1. Support Stomach Acid

Reflux, heartburn and bloating from intense training (42) often lead to the prescription of PPI (acid blockers) for athletes (especially runners) to reduce symptoms. However, contrary to popular belief, strenuous exercise actually suppresses natural stomach acid production, further exacerbating digestive distress. To counter this, swig 1-2 tbsp of apple cider vinegar in water with meals or take HCL capsules (43). 

#2. Avoid NSAIDS at All Costs

Drugs like Tylenol, Aspirin and Advil (44) wreak havoc on both liver health, gut lining integrity and a balanced biome. An alternative? Try nature’s Tylenol:

  • Liposomal curcuma longa (curcumin), paired with Boswellia AKBA (frankincense)
  • CBD oil (topical or sublingual)
  • Comfrey cream (for sprains, bruises, broken bones, stress fractures)

#3. Eat Enough Dietary Fiber

Exercise On Gut Health - Healthy Foods With Lots Of Fiber

Aside from consuming fiber directly before and after training. Plenty of fiber included in your other meals throughout the day is imperative for healthy bowel habits—vegetables, fruits and even pre-biotics like properly prepared legumes (soaked prior), prebiotics (properly prepared oats) and resistant starches (like cooked and cooled white rice and potatoes) (45). That said, if gut problems continue after several weeks of pro-active intake of fibers, it may be worth considering a short-term low FODMAP diet (46) while you tackle strategy #5 more directly.

#4. Supplement Smart

Calm inflammation, balance the biome and support gut integrity with quality gut lining and digestive function supports, like aloe vera (juice and supplements) (47), exogenous short chain fatty acids (48), (like tributyrin), colostrum, digestive enzymes, L-glutamine (49) and herbal teas (slippery elm, licorice root, fennel, marshmallow, chamomile, rose hip).

As for protein powders—commonly used in sports performance and fitness marketing, avoid artificial sweeteners, fillers, and funky names of ingredients you can’t pronounce. Also, avoid over-consumption and over-reliance on protein powders as a primary source of protein in the diet, as protein powders can negatively alter healthy gut bacteria by naturally decreasing carbohydrate and fiber intake and increasing protein intake (50). I typically recommend an easily-digetable hydrolyzed beef isolate protein, colostrum whey (if you tolerate dairy) or a well-vetted plant-based protein if you follow a plant-based diet around workouts (either pre or post)—particularly resistance training— if preferred, but not as a “necessity” as long as you eat enough real protein at meals (approximately 1 gram/pound of bodyweight is a good rule of thumb to stat).

Interestingly, probiotics both before and directly after exercise have not shown significant benefits in athletes in research to date for modifying leaky gut (51, 52, 53). This could be because, if you lead an active lifestyle and keep up the same training habits, they may negate positive shifts in the microbiome with supplements alone (you can’t out supplement a stressful lifestyle). Which is where other gut-modulating factors (like sleep, dietary fiber, food variety, work-rest day balance for fitness) come into play.

#5. Test, Dont Guess

Carbohydrate malabsorption is a common ‘side effect’ of exercise as hydrogen gas is naturally elevated with intensity. Studies in endurance athletes who workout for 3+ hours at a time (such as running or cycling) show that hydrogen levels spike and upwards of 70% of athletes experience carbohydrate malabsorption (both during and after training) (54, 55).These findings may be aligned with more likelihood of SIBO presentation and comorbidities like candida or SIFO (small intestinal fungal overgrowth), explaining continued GI symptoms in athletes until treated appropriately. Similarly, eating disorders—common with overtraining—are a real issue that may need to be addressed as well if you want to heal (considering that up to 98% of individuals with eating disorders also have a functional gut disorder  (56, 57). The good news? Heal your relationship with food and gut problems significantly improve.

Connect with our functional medicine clinic today to get to the root causes of your GI challenges with proper functional gut testing that most conventional doctors do not do, including SIBO testing, comprehensive stool analysis plus parasitology and functional blood chemistry.


Exercise can be both a positive and negative stressor on the gut microbiome and gut health.

However, given the overall health benefits of exercise, the leaky gut and microbial shifts induced by exercise do not outweigh the positive adaptations of exercise on human physiology.

By using these gut-supportive strategies, you can both improve athletic performance, fitness and preserve gut integrity.

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