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A Flexible 9-Step Gut Reset Protocol, From A Functional M.D.

Amy Shah, M.D.
Author: Expert reviewer:
Updated on December 22, 2022
Amy Shah, M.D.
Integrative Medicine Doctor
By Amy Shah, M.D.
Integrative Medicine Doctor
Dr. Amy Shah is a double board certified MD with training from Cornell, Columbia and Harvard Universities. She was named one of mindbodygreen's Top 100 Women In Wellness to Watch in 2015 and has been a guest on many national and local media shows.
Lauren Torrisi-Gorra, M.S., RD
Expert review by
Lauren Torrisi-Gorra, M.S., RD
Registered Dietitian
Lauren Torrisi-Gorra, MS, RD is a registered dietitian, chef, and writer with a love of science and passion for helping people create life-long healthy habits. She has a bachelor’s degree in Communication and Media Studies from Fordham University, a Grand Diplôme in Culinary Arts from the French Culinary Institute, and master's degree in Clinical Nutrition and Dietetics from New York University.
Last updated on December 22, 2022

In my functional medicine practice, I often recommend the following one-day gut reset protocol to my clients to help get their digestion and GI tract back on track. It's particularly helpful after a period of indulgences like special occasions and holidays. Some of the steps might even help address root causes of digestive upset.

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What is a gut reset?

A gut reset, also commonly referred to as a "detox" or "cleanse," aims to restore balance in the human microbiome and the GI tract (a major detoxification organ).

While research on the effects of short-term "detox diets" or "gut cleanses" on the body is limited, with most studies being too small or lacking robust clinical evidence, according to some studies, consuming certain whole foods and nutrients can modulate the removal of toxins from the body1.

Eating a variety of whole foods will provide an array of nutrients and phytonutrients that may help support the body’s intrinsic metabolic detoxification pathways at a mechanistic level, but additional clinical trial research is warranted to elucidate these effects further.

Indeed, detoxification is a 24/7 affair (because that’s how detoxification pathways work in our body), so while targeted periods of gut focus to reset digestive health are useful for many individuals, I’ll let you in on a secret: The gut reset principles below are broadly useful, each and every day, for promoting a healthy GI tract for life. After all, why care for your gut sometimes when you can nourish it daily?

Below, a nine-step routine for keeping your gut healthy and happy.

1. Start with an intermittent fast

Just like you, your gut needs a period of rest and rejuvenation to function optimally.

Giving it a break can support antioxidant and anti-inflammatory processes, cellular cleanup (the fancy word here is “autophagy”)2 and even help shed water weight and ease bloating.

Studies are coming out all the time supporting the benefits of intermittent fasting3, which gives the body a break for a set number of hours each day so that your gut can repair, reset, and rest. Even a seminal research review in the journal 4Cell4 4identifies intermittent fasting as a key pillar of longevity nutrition (i.e., eating for a long, healthy life).

The night before you start your gut reset, plan to fast for 12 to 16 hours. To put this in perspective—a 12-hour fast means you stop eating at 7 in the evening and don't eat again until breakfast the next day at 7 in the morning.


Intermittent fasting has a growing body of evidence-based science for gut and overall health. The night before you start a gut reset protocol, I recommend clients stop eating for 12 to 16 hours.
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2. Begin your morning with water

In my opinion, drinking water, especially room temperature (sans ice) or warm water on an empty stomach, is one of the best things you can do for digestion.

As we know from Ayurvedic principles, warm water is gentle on the GI tract and stimulates digestion5, which naturally helps food move through the digestive tract and promotes the removal of waste.

I recommend you start your detox day with at least one full glass of room-temperature water before you consume any food.


Start your day with at least one full glass of warm water (no ice) before you consume any food to promote hydration (obviously) and digestive pathways.
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3. Have a sugar-free breakfast

In preclinical studies, high-sugar diets promoted metabolic disease, while the elimination of sugar provided protection from obesity and metabolic syndrome6.

To give your gut a break, start by avoiding refined sugars and added sugars in your morning meal (and really in general). Fruit sugars are OK (berries are best), but make sure they're accompanied by plenty of fiber and fat, so you don't spike your blood sugar (and then crash).

Try one of these green smoothie recipes or this MD-approved tofu scramble. These five-ingredient breakfast cookies are a great choice, as is a quinoa breakfast bowl.


Eat a breakfast that is sugar-free (i.e., avoid refined and added sugars) and rich in fiber for gut health and blood sugar balance.
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4. Midmorning, have a cup of chai

In very early studies, researchers have found that the release of tea polyphenols have been shown to help to control the glycemic index and digestibility of starchy foods7.

A mid-morning cup of tea might help digestion when you've had a breakfast that's heavier in starch. Boil 1 cup of water, then add in 1 tablespoon of loose chai tea. Add additional gut-supporting spices like ½ teaspoon each of cinnamon, cardamom, and ginger.

You can also add nutmeg or clove. I like to strain the tea and add a splash of almond or coconut milk for creaminess.


Chai containing gut-supporting ingredients like cinnamon, cardamom, and ginger is what I recommend midmorning.
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5. Have a broth-based meal with probiotics for lunch

The nutrients found in a clean bone broth can help soothe the gut. Bone broth contains the amino acid glutamine (among others), which has been shown to improve intestinal function in preclinical trials8.

Choose bone broth from high-quality, grass-fed animals or a vegetable broth, and add some extra vegetables to it for a filling, gut-friendly meal.

In addition to prebiotic fibers from vegetables, adding 1 tablespoon of fermented foods (like kimchi, sauerkraut, or some pickles) to your meals is another easy way to work gut-friendly bacteria into your life.

Other ideas: Stir 1 teaspoon or less (it packs a punch!) of miso in your soup, or sip on kombucha, non-dairy kefir, or kvass (a fermented cereal-based non-alcoholic beverage) with your meal.

Perhaps easiest, try incorporating a high-quality probiotic into your routine to further bolster your gut-centric diet.


Choose a high-quality bone broth for lunch to help soothe the gut. A probiotic supplement is another good way to work gut-friendly bacteria into your life.*

6. Don't snack between meals

Remember the intermittent fasting discussion before: Giving your gut a break is a big part of this gut reset protocol, whether you try it for over the short- or long-term. Try to limit snacking, and if you're feeling peckish, have another glass of chai or some vegetables with hummus instead.


Limit snacking in order to give your gut a break during the reset.

7. Add prebiotics to your dinner

Hunter-gatherer societies ate roughly 200 grams of fiber daily, while we get approximately 15 grams with a typical modern-day diet. We have a fiber gap!

The best source of fiber is from complex carbohydrates from fermentable plant fibers or "prebiotics," which support good bacteria (microbes) already present in the gut.

The following foods are especially rich in prebiotic fibers:

  • Yams and other tubers
  • Potatoes
  • Ginger
  • Leeks (green and white parts)
  • Fibrous parts of fruit and vegetables
  • Legumes/beans
  • Inulin (chicory, agave)
  • Flaxseeds

Add more cellulose fibers into your diet for contributing bulk to your stool. You can find these insoluble cellulose fibers in the tough parts of veggies and fruit (think of broccoli stalks, the bottom of asparagus, kale stems, and orange pulp).

Try to include at least one serving (extra credit for two or three!) of prebiotic food in your dinner. These spiced stuffed sweet potatoes are a great option, as is this sweet potato breakfast porridge recipe.


Prebiotic fibers support good bacteria present in the gut. Foods like sweet potatoes, ginger, leeks, and beans are especially rich in prebiotics.

8. Minimize stress

Unchecked stress has a negative effect on the gut (and whole-body health). When you're stressed, this can lead to increased inflammatory processes9, gut permeability, visceral hypersensitivity, and gut motility. To minimize stress:

  • Try a mini-meditation: Take three long, deep breaths, with five counts in, and five counts out. Try not to think about anything but the breath going in and then going out. Do this two or three times a day.
  • Do at least five yoga stretches. Moving and stretching your tight muscles can really help get you into a calm state. I recommend a standing stretch, standing forward fold, seated twist, backbend, and a seated forward fold. Forward folds are especially helpful for stress.
  • Think to yourself when you start to get rushed: "I have plenty of time; there is so much time." This will give you the calm to do your task without being rushed. You'll be surprised by how much faster you are when you're calm!
  • When you get angry, repeat this mantra: "I am peaceful. I am happy. I don't let anyone change that." Positive affirmations go a long way.


Stress has a negative effect on the gut. To minimize unwanted stress, try practicing a few minutes of meditation, yoga, breathwork, or positive affirmations to get yourself back in a calm state.

9. Go to bed early

Shortened sleep is associated with an imbalanced gut10. Getting adequate sleep—seven to nine hours a night (depending on the individual!)—helps overall physical and neurological health and has a significant impact on stress levels, which will give your body the rest it needs to reset your gut.


I recommend clocking in at least eight hours of sleep. This can minimize stress and give your body the rest it needs to help reset your gut.

Frequently Asked Questions

What are the best supplements to take to support your gut?

There are many different supplement options available to support a healthy gut. In general, it's best to start with a good probiotic. Read more about 12 of our top-rated supplements for gut health.

How do I know if I need to heal my gut?

From digestive discomfort to tiredness, there can be a number of signs your gut is out of whack.

How long should I do this for?

Some clients find success with a three-day gut reset routine, while others extend the concepts over the long term as a healthy gut lifestyle. Partner with your healthcare practitioner to personalize an approach that’s right for you.

The takeaway.

My gut health reset features a low-sugar breakfast, fiber-packed lunch, and prebiotic-rich dinner to support your gut's natural detoxification processes. If you can take away just a few of these changes, you'll be setting yourself up for long-term success. Remember: Eat lots of fiber, consume probiotics, add more fermented food to your routine, and get some sleep!

Editor's Note: This article was originally published on January 2, 2017. A previous version of this article indicated that a gut cleanse can remove toxins in the body. We have since clarified that statement to indicate that an overall gut reset can help restore balance in the gut microbiome.

Amy Shah, M.D. author page.
Amy Shah, M.D.
Integrative Medicine Doctor

Dr. Amy Shah is a double board certified MD with training from Cornell, Columbia and Harvard Universities. She was named one of mindbodygreen's Top 100 Women In Wellness to Watch in 2015 and has been a guest on many national and local media shows. She helps busy people transform their health by reducing inflammation and eating more plants, utalizing the power of the microbiome to help digestion, natural hormone balance and food sensitivities. She is an expert on intermittent fasting for women and has a 2 week guided group program.