
Bowel Cleanse: Your Foundational Step for Gut Healing
Over the years, our naturopathic clinic has worked with countless patients seeking relief from chronic gut issues, and one of the most effective starting points has always been a colon (aka bowel) cleanse. We’ve recommended a variety of methods—from simple, at-home techniques to more advanced options like colonic hydrotherapy. I’ll explain them all.
Over more than three decades of clinical practice, we’ve helped thousands of patients in many countries overcome chronic digestive issues. Time and again, one critical step stands out as the cornerstone of gut health: the colon cleanse. Whether you’re struggling with bloating, constipation, irregular bowel movements, or Candida overgrowth, a well-implemented bowel cleanse sets the stage for profound healing. It clears the way.
Clinically-Proven Method for Gut Microbiome Recovery and Health

Restoring gut health is a journey best undertaken with a structured and logical approach, one that prioritises preparation and progression to prevent setbacks and maximise results.
At our naturopathic clinic, we consistently found for many years that following a strategic sequence of cleansing steps avoids common pitfalls while laying the groundwork for profound and lasting gut health improvements.
Rushing into any cleanse without addressing underlying issues—such as irregular bowel function, sluggish digestion, or constipation—can lead to unintended consequences. For instance, attempting liver detoxification before resolving gut imbalances may result in the re-absorption of toxins into an unprepared and inflamed intestinal environment.
This can exacerbate conditions like intestinal permeability (leaky gut) and worsen symptoms rather than alleviating them.
The Bowel First, Then Gut, Then Liver
Our approach focuses on clearing, establishing, building, and maintaining optimal gut microbiome health before advancing to more intensive liver cleansing. By first supporting bowel regularity and addressing gut dysbiosis, the body is better equipped to eliminate Candida overgrowth, bacterial imbalances, or parasitic infections. Our phased-method also provides an opportunity to re-evaluate our diet and lifestyle habits and choices, gradually eliminating irritants in our life and identifying hidden food triggers that might have gone unnoticed—even by other healthcare professionals.
Clinically, we’ve found this systematic approach to be highly effective, not only in resolving chronic or “mystery symptoms” that have eluded diagnosis but also in helping patients regain a sense of control over their health.
It’s the foundation of our enduring success in delivering personalised care, and a key reason many patients in the past turned to us after other many other treatments had fallen short.
By addressing the bowel, gut and liver first, we create a stable platform for deeper cleansing while minimising the risk of relapsing or complication. This thoughtful preparation allows our body to heal gently, thoroughly, and sustainably—restoring balance to the gut microbiome and improving overall health for the long term.
Let’s now discuss the 3 Steps of the Candida Cleansing (Beginner) sequence in brief:
1. The Colon Cleanse (One Week) – The Page You’re On

Start with a gentle Colon Cleanse to clear out accumulated waste, toxins, and harmful microorganisms like yeast, bacteria, and parasites. This short cleanse, helps restore a healthy intestinal barrier, boosts nutrient absorption, and balances the gut microbiome. It also helps reduces the chance of sudden die-off. Probiotics, enzymes, and antifungals can be taken advantageously during this stage to clear unwanted yeast, dysbiotic bacteria, and parasites.
2. The Cleanse Diet (Two Weeks)

The Cleanse Diet follows the Colon Cleanse. By nourishing our gut and body with whole foods, we provide it with essential vitamins, minerals, and antioxidants necessary for healing the gut. During this phase, mindful eating practices are key—listen to your hunger cues, chew thoroughly, enjoy your food. A Cleanse Diet helps us repair our “leaky” gut lining and prepare it for the liver cleanse. Targeted supplements during this phase further cleanse and balance the gut.
3. The Liver Cleanse (One Week)

The Liver Cleanse, the final stage, focuses on detoxifying and revitalising the liver to support healthy digestion and efficient detoxification—key for Candida overgrowth, IBS, or SIBO recovery. This phase activates the liver’s detox pathways, helping the body eliminate toxins, dead yeast, chemical residues, and heavy metals. Antimicrobial supplements, probiotics and enzymes play a crucial role during this third phase of the Candida gut cleanse.
Articles of Interest
The Colon Cleanse
What Is Colon Cleansing?

If you’re experienced with bowel cleansing, you likely know what to expect. But if you’re a first-timer, rest assured—colon cleansing is a straightforward, unobtrusive process that won’t interfere with your work or social life. Done correctly, there’s no need for embarrassment, and no one even has to know. Now that we’ve cleared that up, let’s explore this ancient wellness practice.
Bowel cleansing, also known as colon cleansing, is an age-old method aimed at cleansing the large intestine to promote better health. Often paired with detox programs, it’s a staple in holistic wellness routines recommended by many natural health practitioners. Despite its long-standing use, opinions in the medical and scientific communities remain divided on its necessity and effectiveness for detoxification.

Colon Cleansing Resources
Here is a list of the different resources available for you to guide you through the Colon Cleanse program. Be sure to download and print any relevant documents.
The 4 Benefits Of Colon Cleansing
A colon cleanse is much more than a mere “detox fad” —it can be your clean foundation for restoring digestive balance and harmony. By removing accumulated waste and unwanted microorganisms, we create the perfect environment for gut repair and healing.
Key benefits of a bowel cleanse also include:
Safe and Effective Colon Cleansing
While there are numerous bowel-cleansing methods, we recommend a simple, practical, and sustainable approach. In our program, we emphasise:
For those needing additional support, I suggest colonic hydrotherapy under professional supervision, something we’ll soon discuss.

From Doubt to Discovery: A Shift in Perspective
Scientific skepticism is nothing new in natural medicine. Decades ago, the concept of probiotics and the gut microbiota faced widespread doubt. In the 1960s and 70s, the consensus questioned whether probiotics provided any health benefits, I still recall comments like, “How can bacteria be beneficial?” dominating medical conversations.
Fast forward to 2024, and research has firmly established the critical role of probiotic bacteria and our gut microbiota in promoting gut health and overall well-being. In 2019, almost 600 papers were published alone with reference to the history of our gut microbiome.
Even Candida overgrowth, once dismissed, has gained broader acknowledgment, especially over the past decade. Perhaps eventually colon cleansing, including gut microbiome restoration, like probiotics, may follow a similar trajectory. As new studies continue to emerge, our perceptions may well shift.
For now however, like the past one-hundred years, gut cleansing and microbiome restoration remains a key component in natural health practices, offering tangible benefits for those seeking to support their digestive and overall health. (Graph from Lewandowska-Pietruszka et al., 2022)

100 Hours of Research
Dr. Pizzorno, a well-know expert and natural medicine researcher mentioned after 100 hours looking at scientific evidence, he is convinced gut-derived bowel toxins have substantial clinical relevance. Further stating, the more he looks at research, the more he finds, suggesting we are only seeing the very tip of the iceberg. (Pizzorno 2014)
Before We Go Further, May I Ask A Very Personal Question?
Are you having daily (and easy) bowel motions? Click Yes or No to learn more:
What Do I Need To Complete a Colon Cleanse At Home?
Bowel cleansing can be completed in a number of different ways; however, I suggest you use a powdered dietary supplement, here are a few suggestions:
If you’re considering a colon cleanse, my personal preference is for a magnesium-based cleansing powder. While some products use different herbs or nutrients specifically designed for bowel cleansing, magnesium stands out for its ability to provide a gentle yet effective cleanse. Always follow the instructions on the product label and ensure you stay well-hydrated when taking any colon-cleansing supplement.
The goal of a colon cleanse is to flush out waste, old mucus, and food debris from the large intestine, creating a clean and balanced environment that allows for better nutrient absorption and the growth of beneficial bacteria. This process also helps to reduce the population of unwanted microorganisms in the bowel. It means you’ll need to drink plenty of water, and much less coffee, tea, soda drinks, and especially alcohol.
Finding a natural colon cleanser that is both effective and gentle can be challenging, but magnesium-based powders have proven to be particularly useful for this purpose. They offer a safe, controlled option for cleansing while supporting overall gut health.
How To Do a Colon Cleanse

Use 1 tsp. as one dose. A normal dose of a colon-cleansing magnesium powder is about one teaspoon, but follow the instructions on the container you are using.
We recommend mixing one heaped teaspoon (5 grams) into 250 millilitres (8 ounces) of pure water or your preferred beverage. Stir well and drink immediately.
The Best Bowel Cleansing Tips

Bowel cleansing supplements should be given serious consideration by individuals who are looking for the best outcome when it comes to starting a healthy new diet. A good bowel cleanse sets you up for a successful start when it comes to a new eating plan, especially a diet involving more fresh foods.
Since I’ve not experienced any major issues related to the use of bowel cleansing supplements with patients, I have been recommending magnesium-based cleansing products for many years. I’ve found it is especially helpful to gently cleanse the bowels prior to any cleansing or detoxification programme.
Here are some of my best bowel cleansing tips.
Gut Remedies & Relief Strategies
Download your PDF copy of our excellent guide to Gut Remedies and Relief Strategies. It’s the 4th page of the PDF Bristol Stool Chart and Poop Guide (If you downloaded those resources above, you’ve got it)
You’ll find this one-page guide handy during your beginners Program. Print it off and keep it handy along with your other free documents.
There are many solutions to all the most common issues that may arise during the course of your program
What Is Colonic Hydrotherapy?
According to the International Association for Colon Hydrotherapy, by introducing pure, filtered and temperature-regulated water into the colon, human waste is softened and loosened, resulting in evacuation through natural peristalsis. (I-ACT – The International Association for Colon Hydrotherapy)
Colonic hydrotherapy is a highly effective and gentle water-based therapy. By gently introducing purified and temperature-regulated water into the colon through the rectum, human waste including bacterial/fungal toxic by-products, is softened and loosened, which causes the waste to naturally release through a natural process called peristalsis.
Some people find it strange, colonic hydrotherapy. There’s nothing strange about the incredible benefits most will experience. Here are several reasons why this therapy is so good for our health:
Colonic Hydrotherapy Is Safe And Effective
For most people, attending a colonic hydrotherapy session can be a comfortable and relaxing experience. We have never experienced any problems, in spite of what you may have been told or read online. For the best experience, always consult a registered colonic hydrotherapy health-care professional. Our clinic has referred patients to several we’ve known over the years and they’ve all been wonderful people with a real passion for the work they do
Elimination Of Bowel Toxins Has Clinical Relevance
The elimination of subtle colonic waste build-up is a key objective of colon cleansing, though it’s important to dispel myths surrounding it. Despite exaggerated claims like the colon being “clogged with 50 pounds of waste,” which still circulate online, these misconceptions understandably prompt skepticism from the scientific community.
Bowel cleansing does have its merits when approached properly, despite the misguided statements made by those with limited knowledge of microbiology, intestinal permeability and gut function.
Problems tend to arise when some individuals become overly enthusiastic, opting for excessive or repeated daily bowel cleanses. For example, daily coffee enemas or more extreme home colonic treatments can be harmful if overdone. We’ve observed such cases in our clinic where patients, in their eagerness to cleanse, went way too far. It’s crucial to approach bowel cleansing responsibly to avoid such complications and maintain a balanced, healthy approach to gut care.
Is Cleaning Our Colon A Good Way Of Eliminating Gut Toxins?
Colon cleansing is often used in preparation for medical procedures like colonoscopies, but it’s also promoted by natural and integrative health practitioners for other purposes, such as removing dysbiotic bacteria, yeast toxins, and accumulated waste. Colon cleansing is especially relevant when transitioning from a diet high in ultra-processed foods into a natural whole foods diet.
3 Potential Areas Of Concern With Bowel Cleansing
Please don’t be concerned – If you are thinking about colonic irrigation, it’s best to see a registered colon hydrotherapist rather than try and attempt colonics at home by yourself.
Rebalance Your Gut Flora the Professional Way
Yeastrix Daily Probiotic is designed to address gut challenges head-on. Whether you’re aiming to cleanse your colon, rebalance your gut flora post-antibiotic use, enhance your immune defences, or improve specific areas such as vaginal, urinary, or digestive health, Yeastrix Daily Probiotic offers a potent, scientifically-backed solution.
With targeted strains, high-potency, and a gentle delivery system, Daily Probiotic provides effective, long-lasting benefits for men’s and women’s unique health needs.
Key Product Features:
By integrating these features, Daily Probiotic stands out as a reliable and professional choice for those seeking to enhance their health through targeted probiotic supplementation.
Even Our Smallest Health Habit Is Important
It’s important to define ‘healthy’ and ‘unhealthy’ and set specific goals, like eating more vegetables, cutting back on processed foods, limiting alcohol and coffee, focusing on rest, and drinking enough water every day.
Consistently practicing these fundamental habits, especially staying hydrated, can have a stunning impact on our overall well-being. Still, we frequently pursue the latest trends at the expense of neglecting basic needs, such as proper hydration., it’s crazy but true.
Golden Tip
Here’s a good tip if you are not familiar with bowel cleansing or taking a bowel cleansing product. Be cautious about passing early morning wind (gas) from your bowel unless your bottom is placed over a toilet bowl 😉
Transitioning From Colon Cleansing To Gut Barrier Repair

After completing the colon cleanse, the next phase is repairing the gut lining and encouraging the growth of healthy colonies of beneficial gut bacteria. This is an important stage for people with intestinal permeability, otherwise known as leaky gut syndrome. This involves our second module – the Cleanse Diet that’s rich in healing, antimicrobial, anti-inflammatory, pre-and probiotic foods. It’s also free from gut irritants, it’s clean-up time.
The Cleanse Diet also primes our body for the Liver Cleanse, which encourages the releases of toxins stored in our liver, kidneys, and other body’s tissues.
Studies have consistently found that a diet high in fibre, especially in fruits and vegetables, nuts, seeds, legumes, and whole grains is essential for our body to be able to detoxify substances and overall health. These foods aren’t digested or absorbed but help cleanse the gut by supporting optimal intestinal function (Ioniță-Mîndrican et al;., 2022).
Once our bowel is functioning optimally, and supported by a whole foods diet, our body can more efficiently eliminate toxins over a period of time from deeper stores within our body.
After this cleanse, we shift our focus to identifying and removing any potential anti-nutrients, or food allergens or intolerances, repairing the gut lining—a process crucial for those suffering from leaky gut syndrome. It is at this point some individuals decide on advancing the the Candida Cleanse Advanced program, because it includes more information about identifying and dealing with food triggers. This is especially relevant for those with chronic or recurring Candida overgrowth, IBS, or fungal, bacterial (SIBO) or parasite issues.

A Proven Phased Approach
With over 30 years of experience, we’ve developed a cleansing and detox system that consistently delivers lasting results for chronic and recurring digestive conditions. The key is starting with the colon cleanse, then addressing gut repair and liver detoxification.
Our Candida Cleanse Beginner Program is not just about cleansing—it’s about building a resilient digestive system and a healthier, more vibrant you. Whether you’re a beginner or have tried other gut health programs, this approach can transform your health from the inside out. Take the first step today with confidence—your gut will thank you!

Candida Cleanse Beginners Program
Have you started the Candida Cleanse Beginners Program and now completed the Colon Cleanse? Congratulations!
Click HERE to go back to the Candida Cleanse Beginners Program, download your Cleanse Diet resources and go on to complete the Cleanse Diet.

Eric Bakker N.D.
Greetings! I am a naturopathic physician from New Zealand. Although I’ve retired from clinical practice since 2019, I remain passionate about helping people improve their lives. You’ll find I’m active online with a focus on natural health and wellbeing education through my Facebook page and YouTube channel, including this website.




