Part 2: How to Heal the Gut (and Acne) Naturally- The Step-By-Step

If you haven’t read the backstory of how my body and skin hit rock bottom and the gut symptom checklist, then you can go back and read part 1 HERE. Or if you need a bit of a refresher about the gut-skin connection you’ll want to read this one. But, if you’re primed and ready to go, get excited, because I’m about to show you the step-by-step of how to heal your gut and acne naturally.

Firstly, I want to preface that there are multiple ways to heal the gut – whether it’s SOS free, GAPS, specific carbohydrate diet, low fodmap, medical medium, taking antimicrobials or taking antibiotics. Every method of gut healing has testimonials, but what is amazing for some isn’t good for others. Everyone’s gut is individual and unique.

I am here to set you up with the tools you need. I’m going to show you the exact steps I took to heal my gut (and skin) so that you can make an educated decision about what works for you. Remember, there are many roads to reach a destination, but we all arrive at the same place eventually.

the gut RESET

The 5 phases I went through to heal my gut (and my skin) is what I termed the gut RESET (I mean, who doesn’t love a good alliteration)

the gut RESET: remove, eliminate, seal, expand, thrive

You will notice that through the 5 phases, the diet component will change. Initially the focus is on a gut healing diet – where you are trying to heal and restore a damaged gut – so will require you to remove certain foods temporarily to support this (phases 1-3). However, as your gut begins to heal, your body’s ability to process and digest food dramatically changes and the focus then switches to more of a gut nourishing diet to allow your gut and health to thrive long term (phase 4 & 5).

The RESET Fundamentals

Each phase had specific things I was introducing or removing dependening on what I was targeting. However, in order to heal the gut effectively, I had some cornerstone diet and lifestyle principles that I applied to all stages.


These were the foundational dietary principles for all 5 phases of my healing. During the eliminate and seal phases (phase 2 and 3) I had to add in more specific dietary changes in addition to these fundamentals.

  • Eating ALL warm, cooked foods. No raw salads – my gut was in such a disarray that it needed easy to digest foods. Raw foods take a lot of effort for your digestive system to process (these were reintroduced into phase 4 & 5).
  • Drinking hot water and lemon in the morning to stimulate digestion
  • Not drinking with meals. This dilutes your stomach acid which you need to be firing on all cylinders to digest your food properly (if you’re going to sip make sure it’s room temperature and not cold water)
  • Giving my digestive system a break by allowing 3-4 hours between meals (but also listening to what my body needed). If I did eat in between meals, it would be drinking a cup of healing meat stock (see phase 3).
  • Chewing your food is important to stimulate and assist digestion so the gut doesn’t have to work overtime to breakdown the food. Tip: let yourself be the last one eating and literally put down your fork during the meal to allow you time to breathe and digest.


  • Minimised exercise to gentle yoga/stretching, slow walks. My body had just enough energy to keep me functioning and alive. It is not the time to do a HIIT workout or a reformer pilates class. Give your body the space to heal. In saying that movement is important to keep your lymphatic system moving (a main detox pathway) so I opted for more gentler forms of movement.
  • Sauna (when I could) to aid in the detoxification of the body
  • Reducing exposure to external toxins like perfumes, plastic water bottles, heating in plastics etc, BPAs. Minimising anything that was going to increase toxic load on by body.
  • Dry body brushing to support my lymphatic system

Okay fundamentals down packed? let’s get onto the 5 phases to heal the gut:


This phase focuses on removing external things that are inflaming the gut. This is where you really have to tune into what your body’s telling you – like being your own detective. For me, my skin was the biggest and most obvious sign that something was wrong inside – literally if I ate something my body didn’t like I’d breakout within an hour or the day after. Sometimes it was joined by other symptoms like gut pain, gas, bloating, or diarrhea.

  • The Acne Trigger journal – This was my most important practise in the early stages (even before getting deep into the gut research space) and highly recommend for anyone working out their acne triggers. I kept a journal to document whether any food, drink or point in my menstrual cycle would trigger my breakouts.
  • Eliminate acne triggering/inflammatory foods – In a general sense this was gluten, dairy, inflammatory oils, sugar and peanuts. I also had to remove a lot of other foods that my gut had become sensitive to due to leaky gut and severe bacterial overgrowth (see phase 2).
  • Removed alcohol – it’s just a no-no when you’re doing all that good gut work because it affects multiple systems in your body like your liver, hormones, and gut microbiome. Things like wine were a HUGE acne trigger for me – a triple threat acne-causing cocktail of sugar, bacterial imbalance and high in histamines.
  • Removed caffeine – caffeine doesn’t like me naturally: I’m an oat milk decaf latte kinda girl. But it was important to remove stimulants (even decaf) to help offload my liver and prevent any unwanted hormone fluctuations. Note this is easy for me however if you are a multiple coffees a day type of person, try cutting down to just one to help support your liver an adrenals.
  • Removing hard to digest foods. Nuts and beans contain phytic acid can be very hard to digest for a damaged gut, even if soaked and activated (reintroduced phase 5). Similarly, I removed hard fibres such as psyllium husks which are like a hard toilet brush cleaner to a damaged gut wall.


This phase generally lasts as long as the medication or herbal supplement protocol. The main focus is just that: to eliminate and eradicate all the bad bacteria and pathogens living in your gut – I picture it like that iconic scene the Matrix when Neo walks into a building and shoots down the guards in the lobby.

As we know from part 1, my gut was overrun by an army bad microbes (almost no good guys left). So I needed to kick them out and fast. l tackled this via a two-pronged approach: starving them off through diet and a strict antimicrobial regime.

Note – I cannot stress how important it is to get comprehensive gut tests done to see what’s exactly going on in your gut. That way you can target the specific pathogens that are living inside instead of throwing grenades at it blindly. This was the most recent test I conducted – this was the best I’ve ever done (and I’ve done a few). Also done through this company; microbiota which does a great visual representation and pointers for those that don’t totally nerd out over this stuff.

The Die-Off Reactions – I want to preface that sometimes your body can feel a bit worse before it starts to feel better. This is because the endotoxins released from the dying bacteria can exacerbate symptoms. I broke out a bit worse before it started clearing dramatically. This is why sometimes people go slower and ease into this elimination phase. I was very strict around taking the supplements to support my liver and mop-op any toxins generated from the die-off (see below).


Okay, don’t get overwhelmed, I was taking a LOT. I chose ‘the go hard or go home’ approach because I literally had nothing left to lose. I was taking multiple supplements to counterbalance everything and make sure my body didn’t freak out on me. However, it is common to start on lower doses and gradually it build up to prevent the die-off reactions (a reaction that occurs from the toxins being released when the pathogens die).

  • Biofilm Disrupter – The microbes in our gut produce a sticky, glue like layer of material known as biofilm that helps the bacteria stick together and creates a safe environment for them to flourish. Think of it like a force-field that stops medication or antimicrobials from attacking it. In order to kill off the pathogen, you must first breakdown down this force-field. This was the biofilm disrupter I used (however there would be multiple on the market):
  • Saccharomyces Boulardii (SB probiotic)  – non-pathogenic, stomach-acid resistant strain of yeast that enhances the immune response, push out the bad pathogens from the gut and help establish the normal microflora [1].
  • Antimicrobials to target the specific parasites and pathogens. Things like oil of oregano, wormwood complex, citricidal (aka grapefruit extract compound).
  • Liver support – to support the liver’s detox pathways by helping remove all the toxins produced by the dying bacteria. If the liver is struggling, it will push these toxins out through your largest elimination organ – your skin. Hello acne.
  • Mop-Up – activated charcoal, bentonite clay and enterosgel bind to the endotoxins released from dying pathogens. This is key to make sure you don’t feel like shit during the elimination process (and don’t get any extra breakouts on your skin through toxin release).
  • Digestive Enzymes – When your gut is compromised, you need all the help you can get to help breakdown the food you’re eating. I took supplements like ox-bile to aid in the digestion of fat and a digestive enzyme that would help me break down proteins.
  • Magnesium oxide – non-habit forming laxative-like supplement to ensure I was going to the toilet frequently. It’s SO important to make sure you are removing the waste from your body so toxins and hormones aren’t reabsorbed.


This is where people get confused and the experts are divided. What do I eat?! Some say to starve out the bad gut bacteria by removing their food supply. Others say to feed them just enough so they don’t go into hiding.

The diet component is all about listening to your unique body. For example, eating carbs may exacerbate symptoms for you, but for others, low-carb/high fat may flare up the symptoms instead.

For me, I followed my own protocol – I started doing a modified version of the gaps intro diet where I consumed a lot of meat stocks (see phase 3 below) and easy to digest foods. With this, I was essentially eating a low-carbohydrate and low fodmap diet which was starving out the bacteria whilst also hitting it with the antimicrobials.

I was still able to eat a small amount of FODMAP foods (these are the foods that the bacteria love) without causing symptoms. It was a balancing act between starving out the bacteria and eating enough food to sustain me (and any good bacteria in there) whilst not exacerbating symptoms. Again, it’s all about listening to your body and how foods make you feel.

Note – you’ll probably find that removing certain foods might help reduce your acne or digestive symptoms but the foods your eating aren’t the problem. It’s your body’s reactions to those foods because of what is going on inside you at this current moment. Removing these triggering foods from your diet is key to allow your body time to heal instead of continually throwing knives at it. But it’s not going to solve the root cause – it’s managing the symptoms. Once we give your body the support and time it needs to heal, the food reintroduction begins (see phase 4).


I had leaky gut which was causing all sorts of inflammatory, malnutrition issues in my gut. So this stage is all about sealing and healing the lining of the gut. Think of it like putting fresh plaster over a wall that is covered in leaking holes.

Healing a leaky gut is like plastering up a hole in a leaky wall

I did this phase at the same time as phase 2 (but split it up for the simplicity of this article). However, it cannot be done before phase 2. If you tackle this stage first and still have an army of bad bacteria in your gut, they are only going to keep damaging the cells of your gut wall making any healing obsolete.


  • Gut Healing – I used combination formulas of all the anti-inflammatory gut healing herbs and powders when I was healing my leaky gut. Better bang for your buck instead of using isolated ingredients. These were the gut healing supplements I tried and loved during my healing (used at different times as they have similar and overlapping formulas): GI Revive ; Eagle – Cytopro repair; Nutrition Care – Gut Relief.
  • Lactobacillus acidophilus (L. acidophilus) (dairy free) – I started incorporating this probiotic towards the end of my rounds of antimicrobials (in phase 2). This specific strain is an important small intestine bacteria that will stop the colonisation of pathogens as well as aid in the absorption of nutrients. I then transitioned to a broader spectrum probiotic in phase 4.


Similar to phase 2, it was all about consuming healing, easy to digest, nourishing foods whilst still eliminating foods that would inflame or feed the bacteria I was trying to destroy. Incorporating a lot of things like soups, vegetable stews and having meat stocks at every meal

  • Meat stocks – the cornerstone of gut healing (and a fundamental part of the healing diet) as they provide the most amount of collagen proteins and gelatin to repair the intestinal wall. This sounds similar to bone broths but is actually very different. Meat stocks are cooking the raw cartilaginous bones and joints with meat still on them (e.g whole chickens, osso bucco, lamb shanks) for short periods of time vs a bone broth which uses the old already cooked bones and cooks them for over 12-24 hours. Meat stocks are the healing liquid gold you need in your life when your gut is damaged. I would be consuming this as the base of every meal and in between meals 


You’ve done the hard work to get rid of the bad guys, now we want to make sure we’re adding all those good guys back into your gut and feeding them with the foods they need to survive (the foods you removed in the initial phases).


  • Broad spectrum probiotic – this is where we want to bring in the good guys back!! Consuming a broad spectrum probiotic to help repopulate the gut. Some examples include, Just Thrive (a spore-based probiotic) or Gutbiome Symbiotic Powder. Notedepending on the test results of your gut, you might need a specific probiotic strain tailored to your gut.


It’s time to bring back the food!! This is where i transitioned off my modified GAPS/low-fodmap diet and slowly reintroduced the spectrum of foods.

I know this can be a little bit scary, especially because these foods caused you pain, or broke you out with rashes or acne. But where a lot of people go wrong is they don’t reintroduce certain foods back into their diet and they stay on a low fodmap/low fructose/low carb diet long-term. Permanently restricting these foods are dangerous and damaging to your bacterial ecosystem long term. You end up starving them of the foods they need to thrive and limiting the diversity of your bacteria. Bacterial diversity if KEY for a healthy gut and skin.

My initial reintroduction focus was on bringing back foods that would feed my new good bacteria so they could make a permanent home inside my gut. This included fibrous and prebiotic vegetables, low fructose whole fruits and resistant starches. Then also bringing back more gluten-free grains, legumes etc.

Tip: When you re-introduce food, it is important to go low and slow. What I mean is, don’t get excited and start introducing everything all in one meal or on one day because if your body reacts you won’t be able to determine which food item was the issue. Introduce one variable at a time and incrementally build up the quantity – you don’t want to overwhelm the body. You need to give it time to adapt to these new foods.

It honestly took me months to build my body back up to eating things I once reacted to (avocados, oh how I missed you!!). You have to be patient, but it’s the most exciting phase after ALL the hard work you’ve done.


This phase is the long-term maintenance phase. It’s about continually feeding your body with wholefood ingredients that will support your hormones, gut and the little micro-organisms inside you.


  • A long-term focus on eating a minimally processed, wholefood, diverse diet with an abundance of plants of all colours, gluten-free wholegrains, legumes and a small amount of organic, high quality animal protein in the week (my body still thrives consuming animal protein, though I know this is not for everybody). My plate is always a beautiful balance of high-quality fats, protein and complex carbs with the majority of my plate an array of non-starchy vegetables (literally if there’s no green on my plate, it’s not a meal).
  • Include prebiotic and probiotic foods, fibrous vegetables and resistant starches to keep those good bacteria thriving.
  • Continue to avoid inflammatory foods like gluten, processed foods, refined sugars, and inflammatory oils (dairy is still a large trigger for my acne so I also avoid)
  • Soak my nuts and grains to reduce the phytic acid and make it easier for my body to digest.

It’s a Holistic Approach. Once I got my gut in better shape, I could then start working on my other body systems like my hormones and re-introducing my bigger acne triggers into my diet like wine, desserts and high fructose fruits.

And that’s it!! That’s the 5 stages. A question you might be wondering is:


For me it took over a year, however I could see drastic change in my body and skin within a few months.

Saying that, every person is individual. My timeframe is not your timeframe. Mine took a long time because of how bad my gut was and having to rebuild my body up from a severely malnutrition state.

Gut health is more than just a hit it and quit it kind of deal – it’s constant process. It’s a lifestyle. Once you’ve healed the imbalances in your gut, it’s about making the right choices for your gut and skin majority of the time (I never prescribe to the strict, regimented, must be perfect 100% of the time lifestyles). It’s about supporting your gut through a whole-body approach with diet, exercise, stress management, sleep and minimising environmental toxins.

And take it from me, once you heal your gut, you can finally heal your skin.

End note: My protocol was designed according to my specific bacterial imbalances in the body. And though my protocol provides a framework that works, it’s SO important to get your individual gut testing done to work out exactly what is happening in your gut and then work with a functional medicine practitioner for the specific supplements you need for your unique body. Test it don’t guess it!   

Nothing in this article is sponsored. Just everything I used to provide you with this most informed information. 


1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3296087/

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