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If you’ve been diagnosed with SIBO and decided to do some research on how to get rid of it, you have probably come across the Bi-Phasic Diet at least once. Like any elimination diet, there is a lot of misinformation and misunderstanding around how this diet is supposed to be used. 

This article is going to break down what the Bi-Phasic diet is and how it came to be, what makes it so controversial, and some best practices for treating/managing your SIBO long-term.

So buckle up, we’re about to get REAL!

Note: This post was originally written in 2021 and has been updated in 2024.

What is SIBO?

SIBO, or small intestinal bacteria overgrowth, is when too much bacteria is present in the small intestine. This is an issue because your small intestine is where the majority of your digestion and absorption happens and should be almost completely sterile. (1)

This overgrowth of bacteria leads to carbohydrate fermentation, which leads to gas production as a byproduct. This leads to uncomfortable symptoms, such as bloat, changes to bowel frequency and consistency, foul smelling gas, and even food sensitivities and skin reactions.

Check out our deep dive into SIBO, the differences between the three types, how to test for it, and how to treat it.

What is The Bi-Phasic Diet?

The SIBO Bi-Phasic Diet was created by a leading doctor in SIBO research and treatment,Dr. Nirala Jacobi. It is based on another naturopathic doctor’s guide, called the SIBO Specific Food Guide, and is designed to get rid of all of the unwanted bacteria in the small intestines.

The best SIBO treatment plan is designed to take you through several phases of treatment. The first phase should always involve laying a solid foundation of “gut happy habits”. These include eating in a calm and relaxed environment, thoroughly chewing every bite, supporting regular bowel movements, stress management, adequate hydration, etc.

This also includes identifying and addressing the root cause, i.e. the reason the SIBO developed in the first place (remember, SIBO is symptom not a root cause). Low stomach acid, slow gut motility, hormonal imbalances, mineral imbalances, medications (like birth control), and blood sugar imbalances are all examples of root causes.

The second step is the elimination/”kill” phase, which is meant to do exactly what it sounds like, kill the overgrown bacteria. 

The third, and arguably most important, phase is the repair phase. This phase is intended to repair the damage caused by the overgrowth and is all about sustainability and preventing a SIBO relapse.

The Bi-Phasic Diet is an elimination diet with two phases and is designed to be implemented alongside an herbal/antibiotic treatment protocol during the elimination phase.

How long does the SIBO Bi-Phasic Diet last?

The SIBO bi-phasic diet protocol lasts a total of 8-12 weeks and is broken up into two phases. 

The phases are implemented as follows:

Phase 1 (4-6 weeks):

This phase is designed to “starve” the bacteria that are growing out of control in the small intestine by limiting fermentable starches and fiber. 

You and your healthcare provider should also focus on repairing the intestinal lining (i.e. leaky gut), restoring proper digestion, and continuing to establish those foundational habits. 

Depending on the severity of your symptoms, you will either follow the phase 1 restricted diet or the phase 1 semi-restricted diet. The semi-restricted diet allows for a few more foods to be included based on your tolerance.

Here are the basics of what’s not allowed during Phase 1 (go here for a complete list):

• Dairy
• Starchy vegetables (i.e. white or sweet potatoes)
• Onions, garlic, mushrooms
• Canned fruit in fruit juice
• Legumes/pulses
• All grains (except if practitioner OK’s rice and quinoa)
• Peanuts, chia or flax seeds
• Agave nectar and maple syrup, xylitol
• Palm oil, soybean oil
• Soft drinks and energy drinks
• Wine, beer, dark liquors/spirits

Phase 2 (4-6 weeks):

This is when antimicrobials/antibiotics will come into play. The goal is to kill off any remaining bacteria that were not “starved to death” in Phase 1. 

The diet protocol will become a little more lenient so that the remaining bacteria can grow slightly and the antimicrobials/antibiotics will be more successful. You will also continue to work on addressing the underlying causes and repairing the gut.

Additional foods allowed during Phase 2 include:

• Homemade yogurt, butter and aged cheese (i.e. parmesan and pecorino)
• Small amounts of red, green or brown lentils and lima beans
• Raw cacao
• Tamari, miso, fish sauce

So there you have it, those are the basics. But there is no-one-size-fits-all treatment for SIBO (or any health condition for that matter). The next step is to put our critical thinking caps on and to analyze whether this is the best treatment plan to use.

The Bi-Phasic Diet Controversy

There are four main reasons that the Bi-Phasic Diet is considered controversial. One, it can be misleading. Two, there is an increased risk of nutrient deficiencies. Three, it can lead to disordered eating practices and four, it can contribute to social isolation.

Can be misleading

The controversy is similar to what surrounds any elimination diet, the diet is very restrictive and is often mistaken to be long-term or even life-long.

Many people, myself included, have spent years living in digestion misery, struggling to identify the cause and how to treat it. So it’s understandable that once you find out that you have SIBO, you are willing to follow any diet or suggested treatment plan to find relief. 

However, as outlined above, this diet is meant to only be followed for about 8-12 weeks depending on the severity of the symptoms and the individual’s tolerance to the treatment plan.

Risk of nutrient deficiency

It is also meant to be followed under the supervision of a gut health specialist. This is a critical piece because of the risk for nutrient deficiencies. It is important to remember that nutrient deficiencies don’t present themselves overnight. You also need to know what you’re looking for.

For example, a vitamin D deficiency results in less calcium being absorbed. If this deficiency is long-term it will result in a bone mineralization defect called osteomalacia, or soft bones. This isn’t going to be noticeable to the untrained eye and can have a lifelong impact on your health.

Your practitioner should be monitoring your blood labs and may recommend certain supplements to take while following the treatment plan based on those labs. 

Opportunity for disordered eating

The restrictive nature of the diet also increases the risk of developing an obsessive or disordered relationship with food (or even a full eating disorder). Your practitioner should screen for these thoughts and behaviors throughout the process and be able to provide the necessary support.

Socially isolating

Another point to remember is that following a strict elimination diet long-term can take its toll on your relationships. It can be challenging to participate in family gatherings or nights out with friends and can feel very isolating. Believe it or not, your social/emotional wellbeing is just as important as your physical wellbeing when it comes to resolving your gut issues.

The Healthy Way of Treating Your SIBO

Follow the 4-step process:

1. Identify & Address (the root cause)
2. Eliminate
3. Repair
4. Sustain

Step 1: Identify & Address 

Identifying and addressing the root causes is essential to the SIBO treatment process. If this step is skipped, the risk of relapse increases significantly. 

Remember, SIBO is not a root cause. It’s actually more of a middle-man that develops as a result of poor digestive function, hormone imbalances (like hypothyroidism), high stress lifestyle, low diet diversity, etc. 

This step also involves establishing some foundational diet and lifestyle practices that will set the body up for success long-term. These practices include balancing blood sugars with balanced meals and snacks, eating a variety of plant fibers, incorporating regular gentle movement, adequate hydration, and keeping the bowels moving.

Step 2: Eliminate

It’s important to remember that diet alone can not fix or eliminate SIBO. It is not possible to fully starve the bacteria because if even one bacterium is left behind, it will multiply once fermentable carbs are reintroduced.

The elimination phase requires a combo of addressing the root causes, laying the foundations discussed in the previous section, and antimicrobials/antibiotics. The specific recommendations should be personalized to you.

This phase of the treatment protocol will last anywhere from 8-12 weeks, depending on your symptoms, root causes, and sensitivity to the supplements.

Step 3: Repair

Similar to identifying the root causes, this step is crucial because the overgrowth has likely caused some damage to the gut. 

I no longer recommend any sort of elimination diet with my clients (except in very specific circumstances) and instead work with them to build a robust and diverse diet. I have learned that this is a more sustainable approach that promotes a healthier, more resilient gut overall and is more likely to prevent a SIBO relapse. 

The repair phase will continue to address the root causes and support the “healthy gut” foundations. It will also include some targeted supplements to repair any traces of “leaky gut” and build a diverse gut microbiota. 

This phase will take 8-10 weeks to complete.

Step 4: Sustain

If you and your practitioner decided to follow an elimination diet plan (like the Bi-Phasic Diet), it’s important to remember that this is not a forever diet. The last phase is the reintroduction phase and is arguably the most important.

This is the phase of all elimination diets where you slowly and strategically reintroduce the foods you’ve cut out in order to identify which ones are your triggers. Because – reality check time! – it is highly unlikely that all of the foods you’ve eliminated cause you problems.

This is another reason why it’s soooo important to work with a gut health professional. Because they will know how best to navigate the reintroduction phase while minimizing symptoms. The end goal should always be to be able to comfortably enjoy as diverse a diet as possible.

Lifestyle Changes to Consider

Diet isn’t everything when it comes to cultivating a healthy gut. There are easy lifestyle changes that can make a big difference in your gut health journey.

• Slow down and remove as much stress as possible while eating (your body needs to be in a “rest and digest” state in order to properly digest your food)
• Do 3 rounds of square breathing before each meal
• Chew food until it reaches an applesauce consistency
• Drink at least ½ your body weight in ounces of water per day (between meals)
• Aim for 30g of fiber/day
  • Try cooking veggies for better tolerance
  • Kiwis and chia seeds are great low-FODMAP sources of fiber
• Limit alcohol if you find it triggers symptoms

Final Thoughts

All in all, the Bi-Phasic diet can be incorporated into a healthy and effective SIBO treatment plan, but it’s not going to work all on its own. Find a trusted gut health specialist to help guide and support your journey and stay focused on the big picture. 

The overarching goals should always be to give yourself the tools needed to confidently manage your symptoms, to release yourself from the constant cloud of “food fear” and body distrust, and to enjoy eating with loved ones again.

Feel free to pin this post to share with others!

If you’ve been struggling with SIBO, bloat, constipation or other IBS symptoms and need some insight into your root causes, check out my Why Am I STILL Bloated Quiz!

Remember: this post is for informational purposes only and may not be the best fit for you and your personal situation. It shall not be construed as medical advice. The information and education provided here is not intended or implied to supplement or replace professional medical treatment, advice, and/or diagnosis. Always check with your own physician or medical professional before trying or implementing any information read here.