How to Clean Your Gut: 9 Proven Ways to Improve Digestion

Most so-called cleanses aren’t worth your money, but lifestyle habits can boost digestive health. Here’s how to clean your gut naturally without wasting money on gimmicks.

Caitlin Beale, MS, RDN
— Signos
Health & Nutrition Writer
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Updated by

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Science-based and reviewed

December 1, 2023
March 8, 2023
— Updated:

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Gut health. Gut cleanse. Gut detox. You’ve heard these buzzwords by now, but what do they really mean? Your gastrointestinal (GI) tract includes everything from your mouth to your anus, but most people talking about gut health refer to the microbiome-rich area of your colon. 

Your microbiome includes your gut's trillions of bacteria, fungi, and viruses. When healthy and balanced, these organisms support digestion, immunity, mood, and overall health. But digestive symptoms and health issues can arise when it’s out of balance.¹

Let’s set things straight: Most people don’t need a targeted colon cleanse. Instead, daily habits that promote healthy digestion are the secret to balanced gut bacteria and a healthy gut. But where did the idea of colon cleansing start, and are there any health benefits? This article will take a closer look.

What is a Gut Cleanse?

A gut cleanse is a treatment advertised to remove toxins or build-up within the colon (your large intestine) to benefit digestive health, weight loss, and overall wellness.

Much of the information you see on social media or online surrounding digestive system cleanses comes from companies trying to sell you “detox” teas, powders, or supplements. You may also see advertisements selling expensive treatments from spas or clinics that claim to cleanse the colon and detoxify the body with colonic irrigations or enemas. 

While these treatments have existed for thousands of years in different forms, the truth is they aren’t based on science.

Let’s step back and talk about what’s inside your colon. The trillions of microbes that live within the walls of your large intestine mean it’s anything but “clean.” These friendly bacteria work together to digest food, synthesize vitamins and other beneficial metabolic byproducts like short-chain fatty acids (SCFA), maintain immune health, and so much more.²

Why Do People Opt For Gut Cleanses?

People seek out gut support and may be interested in colon cleanses if they experience:

  • Food sensitivities
  • Bloating and gas
  • Diarrhea
  • Constipation
  • Joint pain or inflammation
  • Migraines
  • Hormone balance
  • Fatigue

While it’s true that all of these symptoms connect to gut health, most powders or cleanses do little more than help you have bowel movements.

Colonics from wellness centers are also very different from enemas provided by a doctor, which may be necessary for severe cases of constipation.

There are targeted approaches to each of these issues, but if you’re struggling to determine the root cause or why you have these symptoms in the first place, there is a better place to start.


A History of Colon Cleansing: Autointoxication

Gut cleansing has existed since ancient Egypt (and possibly before). Still, the idea took off in the late 19th century as physicians became interested in the influence of intestinal bacteria on health.

Autointoxication is a theory that suggests gut bacteria, in combination with remnants of protein digestion that rotted in the colon, causes harm when absorbed by triggering internal poisoning.³

The concept that food residue rots within the intestines without proper cleaning was discredited in the 1930s. However, some still tried to profit off selling promises of better health with colon cleansing, including unsafe irrigation practices.³

Given that our health depends on the symbiotic relationship with bacteria, it may be more correct to say that people seeking a colon cleanse may need a colon rebalance.

Are There Colon Cleanse Benefits

Gut health conditions are real, but the causes are not from undigested food particles. Dysbiosis (gut bacteria imbalance), inflammation, and intestinal permeability (i.e., a leaky gut) are all explanations for gut imbalances that were not well understood when the idea of autointoxication was developed.⁴

If someone is constipated and needs help to have regular bowel movements, then certain supplements or dietary changes could help. However, the answer to better digestion and overall health isn’t generally found in a bottle of supplements or powders.

Potential Side Effects of a Colon Cleanse

Aside from wasting money, there are potential risks associated with colon cleanses. Supplements may not be third-party or FDA-tested and could contain hidden ingredients. Sometimes the laxative effects can be severe and cause cramping, dehydration, or electrolyte imbalances. 

Colon irrigations or enemas increase the risk of an electrolyte imbalance, dehydration, infection, or damage to the colon or rectum. It could even adversely affect the balance of beneficial bacteria.⁵

Overall, this type of “detox” can worsen your GI symptoms and could cause long-term damage if not done correctly or with medical supervision. 

Gut Detox: 9 Ways to Clean Your Gut Naturally

If a clean gut means a healthy one, you can focus on foods and lifestyle habits that promote gut health. Keeping your gut healthy is not a one-time event, as your body naturally detoxes through a complex system of organs, cells, and enzymes daily.


Here’s how to clean your gut naturally:

  • Choose unprocessed whole foods whenever possible. A nutrient-dense diet is foundational for gut health. Ultra-processed foods are linked to inflammation in the gut which can contribute to dysbiosis, food sensitivities, and other gut-related issues.⁶
  • Opt for a high-fiber diet. A functioning gut and optimal detoxification system rely on regular bowel movements. Fiber cleans the gut naturally and is essential for blood sugar regulation and metabolic health.⁷
  • Add probiotics and prebiotics daily. Probiotics are living organisms that add good bacteria to the gut. Prebiotics fuel the gut microbes and keep healthy bacteria populations diverse and robust.⁸ You can find food sources of probiotics and prebiotics in fermented foods, legumes, vegetables, and fruit, or supplements are another option.
  • Get friendly with sulforaphane. Cruciferous vegetables like broccoli, kale, cauliflower, cabbage, and brussels sprouts are rich in sulforaphane. This antioxidant is naturally detoxifying and anti-inflammatory for the gut. It’s also protective against certain cancers and helps modulate hormones.⁹
  • Stay hydrated. Dehydration is a significant contributor to constipation, and you need even more water if you’re eating a high-fiber diet.¹⁰ Keep a water bottle nearby or sip herbal tea or sparkling water throughout the day-whatever helps you drink more.
  • Keep alcohol to a minimum. Alcohol can increase inflammation in the gut and contribute to dysbiosis.¹¹ A drink occasionally isn’t necessarily a problem for everyone, but if you struggle with gut issues, you may want to cut it out.
  • Keep your bowels moving. You can’t have a healthy gut if you don’t have regular bowel movements. The first step is to ensure you eat enough fiber, drink plenty of water, and move your body. But sometimes, it takes a deeper dive as food sensitivities, stress, medications, and other health conditions can also contribute to constipation. 
  • Manage stress. Stress and gut health go hand-in-hand, as your brain and gut are closely connected.¹² Finding ways to relax (meditation, yoga, journaling, long walks) and creating healthy boundaries in your life can all impact your gut.
  • Consider magnesium. Supplements for gut support vary and should be individualized to the person, but magnesium can support those who struggle with irregular bowel movements.¹³ Using magnesium supplements is not recommended if you have diarrhea, but it could help keep things moving if you struggle with constipation.

Best Gut Cleansing Foods

  • Asparagus
  • Flax and chia seeds
  • Broccoli and broccoli sprouts
  • Cauliflower
  • Brussels sprouts
  • Leafy greens
  • Blueberries
  • Fermented foods like sauerkraut or kimchi
  • Ginger
  • Bone broth
  • Chickpeas
  • Collagen
  • Turmeric
  • Olive oil
  • Lentils
  • Yogurt (coconut is a good option if you can’t tolerate dairy)

A caveat to some of these foods is that some people who struggle with digestion or food sensitivities could notice an uptick in symptoms by adding these high-fiber foods.

If this is the case for you, working with a health professional who understands how to support healing your specific health condition so you can tolerate more of these foods again is important.

Learn More About Nutrition and Healthy Eating with Signos’ Expert Advice

Making diet changes can feel overwhelming, but seeing the results in real-time can motivate you to continue these daily habits to support your gut. The Signos app, paired with a continuous glucose monitor, can show you precisely what foods and lifestyle choices affect your blood sugar and metabolic health.

You don’t need to do a “cleanse” to achieve long-term gut health, but rather make slow and sustainable changes that promote a healthy balance of beneficial bacteria, reduce inflammation, and support regular bowel movements.

Find out if Signos is a good fit for you by taking a quick quiz.

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Topics discussed in this article:


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About the author

Caitlin Beale is a registered dietitian and nutrition writer with a master’s degree in nutrition. She has a background in acute care, integrative wellness, and clinical nutrition.

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