A Step-by-Step Guide to Resetting Your Gut

We start with a short modified fast, either a broth or a cleansing lemonade, taken for two to four days. This gives the gut a brief break and tends to calm symptoms quickly. Most people notice improvements in energy, mental clarity, digestion, and mood by the second day.

From there, we transition into a gut-healing diet. Rather than prescribing one diet for everyone, we work through options in order:

• Start with the Paleo Diet Guide for two to three weeks.
• If that only partially helps, layer in the Low FODMAP Diet Guide.
• If Paleo doesn’t help at all, move directly to a standard low FODMAP approach instead.
• The most restrictive options, autoimmune Paleo or low FODMAP with SCD, are reserved for cases that need more.

Alongside diet, step 1 covers the lifestyle fundamentals that support healing: sleep, sun exposure, time outdoors, movement, and stress management.

This step doesn’t call for supplements. It’s diet and lifestyle only, and for many people, it’s enough on its own.

If you’re not fully improved after step 1, step 2 layers in four categories of support. Everything here continues through the rest of the plan unless noted otherwise.

Give this step two to three weeks before reassessing. Feeling much better, move to step 5. Only partially improved, continue to step 3.

Step 3 targets unwanted bacterial, fungal, or parasitic overgrowth using herbal antimicrobials, layered in three levels depending on how you respond. Everything from step 2 continues throughout, since it helps the antimicrobials work more effectively.

Level 3 isn’t a consolation prize for when the herbs don’t work, it’s a genuinely different mechanism worth choosing on its own merits. The small intestine houses most of your immune system and is especially prone to injury, and an elemental diet has an outsized, favorable effect there specifically. It gives the gut a complete break from digesting solid food while still providing full nutrition, which is reparative, antibacterial, and anti-inflammatory in a way herbs alone don’t replicate. It’s the right call for anyone who reacts to the herbal antimicrobials, and it’s also simply the better-fitting tool for some people from the start. It can be used short-term as a reset, as a full replacement for one to three weeks, or blended with regular meals over the longer term.

Optional add-on: Magnesium Citrate for anyone still dealing with constipation at this stage.

Reassess after roughly two months. Feeling great, move to step 4. Feeling partially better, move up to level 2. Feeling the same or worse, level 3 is usually the better fit.

Once the removal phase is done, the gut ecosystem generally starts to rebalance on its own. Step 4 gives it a nudge in the right direction with a prokinetic, a supplement that supports healthy motility so food moves through the digestive tract at the right pace and bacteria don’t have the chance to overgrow again.

Prokinetic options: Motility Support or Iberogast, either one taken once before bed or split into smaller doses through the day.

Everything from step 2 continues here: probiotics, digestive enzymes, and adrenal support if you’re using it. Stay in step 4 for one to four months. Some people notice little change day to day since a prokinetic is more of a preventive measure, but staying on it now helps hold the progress made in step 3.

With the gut healthier and more stable, step 5 is where we systematically widen the diet back out. Whatever combination of steps brought you here, this step is for everyone.

The approach: reintroduce the most restrictive category of foods first (working back down from wherever you landed on the diet spectrum), one food at a time, with a few servings over a few days, so any reaction is easy to trace back to its source. As carbs are reintroduced, pay attention to how you feel and adjust intake up or down accordingly rather than targeting a specific number.

No new products are introduced in this step. It’s about testing boundaries with food, not supplements, and it’s normal for that process to take anywhere from a couple of weeks to a couple of months.

Once the diet has been widened, step 6 adds targeted feeding for the beneficial bacteria that are now established. This step carries a slightly higher chance of a reaction for anyone who needed the full step 3–4 protocol, so it’s worth moving through it a little more slowly if that’s you.

Step 7 is about finding the smallest program that holds your results. It’s easy for a supplement list to grow over time without anyone checking whether each item is still earning its place, so this step is a deliberate check-in.

No new products here. Instead, work backward through what’s already been added, generally in this order: adrenal support, then the prokinetic, then any antimicrobials, then fiber and prebiotics, then digestive enzymes, and probiotics last. Come off one item at a time, wait one to three weeks, and watch for any symptoms returning. If something was genuinely helping, you’ll usually notice within a few days of stopping it.

The final step is about settling into a sustainable, long-term routine, one that’s usually much lighter than what came before. A typical maintenance plan might include a daily probiotic, occasional Vitamin D with K2 in the fall and winter, Digestive Enzyme with HCl with larger meals, and an occasional day of the modified fast if your gut needs a reset.

Setbacks are normal. When one happens, the fastest way back is usually to briefly revisit whatever helped most the first time through, whether that was diet, probiotics, or an antimicrobial round, rather than starting over from scratch.