These are the most common tell-tale signs of an unhealthy gut to pay attention to. Because your microbiome affects immunity, hormones, nutrient levels, energy, and more — when the gut is off, everything else is impacted.

Reading Time: 8 minutes

The 10 signs of an unhealthy gut provide important insight into how well your microbiome is functioning and whether deeper imbalances are present. These warning signs help reveal connections between gut dysfunction and the rest of the body. As we know in functional medicine, the health of the gut microbiome influences immune resilience, hormone balance, nutrient status, detoxification, and overall vitality. When the gut becomes compromised, it can initiate a systemic domino effect.

WHAT IS THE GUT MICROBIOME?

The gut microbiome is home to trillions of microbes, including bacteria, fungi, and viruses, that live in your gastrointestinal tract. It plays a vital role in many bodily systems, like digestion, immunity, detoxification, and even mental health. 

HOW THE GUT MICROBIOME AFFECTS YOUR HEALTH

Did you know that 70% of your immune system is housed within your gut microbiome? This means that your gut has the power to greatly affect many of the body’s functions, including, but not limited to, immune function. 

The well-being and integrity of your gut microbiome impacts:

• Nutrient absorption and vitamin synthesis
• Detoxification
• Digestion
• Drainage and elimination 
• Mental health and neurotransmitter production
• The gut-brain-skin-hormone connection
• Inflammation regulation

The health of your gut microbiome can influence many health factors, which is why it’s critical to take good care of it. In fact, many health professionals believe that many chronic illnesses stem from an unhealthy gut. 

10 SIGNS OF AN UNHEALTHY GUT

When your gut is dysfunctional and unhealthy, it will find ways to tell you. While some signs are more obvious than others, your body is always looking for ways to communicate when something is off. 

The following symptoms may indicate deeper imbalances associated with gut dysfunction. Because your microbiome affects immunity, hormones, nutrient levels, energy, and more — when the gut is off, everything else is impacted.

These are the most common tell-tale signs of an unhealthy gut to pay attention to:

1. Bloating

Mild bloating can be normal after eating meals or snacks. When it comes to an unhealthy gut, bloating can be extreme. It isn’t always limited to after meals and can occur for no rhyme or reason. This kind of bloating is often driven by gut flora imbalance, fermentation, or SIBO.

2. Chronic Fatigue

Mild levels of fatigue can be normal or due to another underlying condition. The fatigue associated with an unhealthy gut is chronic and usually unbearable. When it comes to an unhealthy gut, chronic inflammation and Leaky Gut are responsible for draining your energy. 

Additionally, poor microbial health can cause blood sugar imbalances and mitochondrial burnout, worsening fatigue. 

3. Skin Issues

The gut-skin axis explains the strong, prominent connection between your gut and skin. Problematic skin, such as eczema, acne, and rosacea, is linked to Leaky Gut and gut dysbiosis. Simply put: a damaged gut leads to damaged skin. In many cases, poor gut function can clog detox pathways, exacerbating problematic skin or flare-ups.

4. Headaches & Migraines

Recurring or chronic headaches or migraines are a bright red flag that something in the body is off. Not only does chronic inflammation (stemming from an unhealthy gut) fuel head tension, it also worsens food sensitivities, histamine load, and serotonin imbalances– all of which can cause throbbing headaches or migraines. 

Unfortunately, the gut is often overlooked in the context of neurological symptoms. However, as with the gut-skin axis, the gut-brain axis explains the strong connection between the stomach and the brain. The two have drastic impacts on one another! 

5. Constipation or Diarrhea

Did you know your bowel movements can tell you a lot about your overall gut health? The consistency, timing, and color of your stool are very telling. Chronic cases of constipation and/or diarrhea are a cue that the gut is struggling. This is often due to underlying parasites or gut infections, SIBO, reduced motility, poor drainage elimination pathways, or inadequate bile flow. 

6. Stomach Pain

Frequent cases of stomach pain are problematic. While it’s normal to experience stomach pain here and there, frequent symptoms are a red flag. It’s important to pay attention to sharp pains rather than dull or cramping sensations. Different types of pain can signal other issues. Common causes of stomach pain include enzyme deficiencies, gut infections, and food reactivity.

7. Autoimmunity

The presence of Leaky Gut often confuses the immune system. This can lead to cases of autoimmunity. A loose, damaged gut lining exacerbates chronic inflammation throughout the body. It can also cause antigen overload, which contributes to the onset of autoimmunity. This explains why healing the gut is often the first step in reversing autoimmunity (and why it plays such a large role in my personalized 1:1 coaching program, using the Abounding 5 Method™. 

8. Sugar Cravings

Pathogenic or harmful gut bacteria feed on sugar. Hence, an overgrowth of bad gut bugs and yeast can incite sugar cravings. Dysbiosis, or an imbalance gut microbiome, can also trigger imbalanced blood sugar levels and affect the production of neurotransmitters, such as dopamine and serotonin.

9. Insomnia & Sleep Trouble

If you find yourself tossing and turning or lying wide awake at night, your gut might be to blame. The production of melatonin and serotonin begins in your gut, and both neurotransmitters help the body prepare for and achieve a good night’s sleep. 

Additionally, dysbiosis in the gut microbiome can lead to nighttime cortisol spikes and blood sugar crashes, disrupting your sleep. When your gut is balanced, your sleep should be deep and restorative. 

10. Anxiety & Depression

In addition to its impact on headaches and migraines, the gut-brain axis affects our emotional and mental well-being. Over 90% of serotonin is made in the gut. When the gut is inflamed and “leaky”, serotonin levels can dive. 

The result? Often, depression, anxiety, and other mood disorders occur. Despite what Western medicine says, healing your gut is the first step in shifting your mental health, and the thing that impacts the clients I work with the most. 

If you experience any of these 10 signs of an unhealthy gut, it might be time to take a deeper look at what’s going on within your gut. While any of these symptoms are “common,” they are far from normal. 

WHAT’S DAMAGING THE GUT IN THE FIRST PLACE?

There are many factors that contribute to the function (or dysfunction) of your gut– many of which are very prevalent in our environment today. However, the most detrimental factors to your gut’s wellbeing include:

• Overuse of medications, like antibiotics and acid blockers
• Chronic stress
• Inadequate sleep
• Poor diet (including ultra-processed foods, artificial sweeteners, inflammatory foods, etc.)
• Environmental toxins and EMF’s
• Mold
• Heavy metals 
• Underlying infections (like SIBO, Candida, and parasites)
• Food sensitivities
• Nutrient deficiencies such as zinc, antioxidants, and amino acids

It’s critical to take inventory of the factors that could be negatively impacting your gut so you can start making the necessary changes. 

WHEN AN UNHEALTHY GUT IS A LEAKY GUT

Many of the factors above can lead to a condition known as Leaky Gut, one of the most common root causes of the 10 signs of an unhealthy gut. Leaky Gut occurs when the tight junctions of the intestinal lining become loose or damaged, allowing partially digested food particles, toxins, and microbes to pass into the bloodstream. This breach triggers chronic inflammation, disrupts immune function, and places stress on your detox organs. 

Over time, Leaky Gut contributes to symptoms far beyond digestion — including fatigue, skin issues, autoimmune flares, hormonal imbalances, and mood changes. Supporting and repairing the gut lining is one of the most critical steps in restoring long-term gut health and overall vitality! 

HOW TO TEST FOR AN UNHEALTHY GUT 

While symptom analysis and identifying the 10 signs of an unhealthy gut are significant first steps, pinpointing where to focus next, it is essential to use functional testing to determine exactly what is going wrong within the gut. This is the only way to address your unique dysfunctions and imbalances and create a personalized roadmap to building a resilient, healthy gut! 

My favorite advanced functional tests for gut health include:

• Functional stool testing (GI-MAP)
• Food Sensitivity Testing (MRT LEAP 176) 
• Micronutrient Testing 
• Zonulin/Wheat Zoomer
• Functional Wellness Panel 
• Blood markers of inflammation

Depending on your symptoms, one or more tests may be sufficient to address your gut issues. Working with a qualified functional medicine practitioner is the best way to use these tests and address any gut dysfunctions.

THE FUNCTIONAL MEDICINE APPROACH TO GUT HEALING

A functional medicine approach looks at the whole picture. In other words, it is a root cause approach to healing your gut. My unique 5-step roadmap, called the Abounding 5 Method™, involves a unique personalized approach that includes:

1. Addressing the vital foundations of health first to activate cellular energy 
2. Uncovering your unique lab data to personalize your plan
3. Supporting and opening drainage and elimination pathways 
4. Optimizing advanced liver detoxification 
5. Restoring and building a resilient gut 

Repairing gut integrity requires a strategic, root-cause approach—one that doesn’t guess or patch symptoms, but rebuilds the gut from the inside out. That’s exactly why I use the Abounding 5™ Method, a proven 5-phase roadmap that restores gut integrity step-by-step. 

We begin with Cellular Energy Activation, ensuring your cells have the nutrients and mitochondrial support needed to repair the gut lining. 

Next, Lab-Guided Precision identifies the exact imbalances—such as infections, food sensitivities, dysbiosis, or inflammation—that are driving leaky gut. 

From there, we move into Elimination Pathways, opening drainage and detox pathways so the body can remove toxins and metabolic waste without overwhelming the gut. 

In Absorption & Detox Optimization, we support digestion, nutrient uptake, and liver function using targeted nutrients like zinc, glutamine, omega-3s, collagen, and polyphenols. 

Finally, Resilient Gut Restoration focuses on repairing the gut lining, rebuilding the microbiome, and restoring long-term balance so your gut can stay strong and resilient—even when life gets stressful. 

In my personalized 1:1 coaching program, we cover all of these steps, and more, which is why hundreds of women have been able to restore their gut, achieve boundless energy, and reclaim their vitality so they can show up fully for what matters most. 

With this structured, personalized approach, true gut repair becomes not only possible—but sustainable. To learn more about the program and to see if it is right for you, check it out here! 

WRAPPING IT ALL UP

These 10 signs of an unhealthy gut can help you identify if you need to look deeper into the gut as a root cause of your ongoing symptoms. As previously stated, when something is off in the body, it will find ways to tell you. These common symptoms are not normal or random. And in many cases, the symptoms of an unhealthy gut reach far beyond the gut itself. 

The good news: you don’t have to live with these uncomfortable or debilitating symptoms anymore! My personalized 1:1 coaching program with the Abounding 5™ Method might just be the customized, one-on-one program you’ve been searching for! 

READ THE LATEST BLOG POSTS:

• 10 Warning Signs of an Unhealthy Gut (+ What to Do About It)
• 10 Signs Your Liver Needs Detoxing (and How Supporting Gut Health Helps)
• Healthy Fall Side Dish Recipe: Braised Maple Dandelion Greens
• Quick and Easy AIP Breakfast Ideas for More Energy Throughout the Day
• Vitamins for Menopause Fatigue: How to Boost Energy and Feel Your Best