How To Heal Your Gut & Rebuild Immunity After Antibiotics

By Marilee Nelson | 03/27/2025

It’s finally Spring! And if you or your children made it through the winter without antibiotics, consider yourselves fortunate (but keep reading!).

For everyone else who suffered through intense ear infections, strep, walking pneumonia, and other ailments that required antibiotics, this article is for YOU.

Here, we’ll share nine simple and accessible ways to heal your gut after antibiotics and restore optimal immune function.

I’ll also share my favorite probiotics for antibiotics and talk about some natural alternatives, too, and when these may be appropriate.

Before We Start, Let’s Address The Elephant In The Room…

Before we get into this topic, I want to say I understand how hard it is for parents---especially the very health-conscious---to give their children antibiotics in the first place.

Although these drugs can be necessary and even life-saving, years of overuse and misuse have led to a lot of skepticism, fear, and even harsh judgments in natural health circles.

To this, I say that yes, antibiotics are definitely still over-prescribed (there’s loads of science to back this up[1][2][3][4]), so it pays to be skeptical, know your natural medicine cabinet, and work with a doctor you really trust.

However, there are times in nearly every person’s life when antibiotics are absolutely appropriate to prevent serious complications or even save a life.

So be kind to yourself (and others), and know you absolutely can rebuild your gut, immunity, and health after taking antibiotics.

The bottom line is that fear is not our friend when it comes to making sound decisions about health (or anything else!), so let your intuition, knowledge, your doctor’s advice, and the evidence guide you to the right decision.

The Pros And Cons Of Taking Antibiotics

There is no doubt that antibiotics have changed the world and saved millions of lives.

Before their discovery in the 1920s, countless people, including babies and small children, died regularly or were permanently disabled from what we now consider very curable diseases.

They were considered a “miracle drug” and thus frequently prescribed for non-bacterial illnesses like colds, flu, and other viruses.

Unfortunately, antibiotics, like all drugs (even miracle ones), have a dark side in terms of side effects.

Although naturopaths, herbalists, and traditional healers had warned about the detriments of over-using antibiotics for decades, it wasn’t until researchers started understanding the gut microbiome that it became clear how devastating overuse can be.[2][3][5][6]

As you probably know, antibiotics act like a nuke, effectively wiping out all harmful and beneficial gut bacteria.

Multiple studies have shown that even one course of antibiotics can completely destroy all or a large portion of beneficial gut bacteria, leading to dysbiosis (dysregulation of gut bacteria and overgrowth of harmful bacteria) and a higher risk of future infection in the short- and long-term.[6][7]

Certain types of antibiotics can also negatively impact genetics and mitochondrial function, disrupt the reproductive microbiome, cause permanent teeth discoloration, tendonitis, and heart problems, and increase the risk of antibiotic resistance.[8][9][10]

This is why it is essential to assess the risk-to-benefit ratio with a doctor you trust and who understands your concerns about over-use.

If you have a dangerous bacterial infection, the benefits definitely outweigh the risks (especially since you can rebuild)!

If you can safely wait a few days and see how things go utilizing natural remedies, then that’s always a great option, so be sure to ask your doctor before accepting a prescription.

For example, many times ear infections can be resolved at home using a watchful-waiting approach,[11] and supporting the body naturally with things like immune-boosting herbs and garlic mullein oil.

However, a cough that doesn’t go away, strep, or a very sick child shouldn’t wait to be assessed by a doctor for the proper treatment.

So, the pros of taking antibiotics are that they effectively wipe out harmful bacteria, help you get better, and may save your life or prevent complications.

The cons are that they also wipe out beneficial bacteria essential for immunity, digestive health, reproductive function, inflammatory response, mental health, and much more, and do nothing for viral infections.

9 Natural Ways To Heal Your Gut After Antibiotics

The general recommendation for healing the gut after antibiotics is to take probiotics.

Although this is good basic advice (and better than doing nothing), a single probiotic supplement (even a multi-strain formula) won’t provide a full spectrum of healing for the microbiome.

The gut, which makes up 70-80% of our immune system, thrives on diversity and benefits from daily challenges presented by various lifestyle factors such as diet, exercise, and time spent in diverse microbial environments.

The overall immune system also benefits from some extra support while the gut is coming back online, which is where herbal remedies and plant-based foods shine!

Here are nine ways to provide full-spectrum healing for your gut post-antibiotics.

1. Take Prebiotics And Probiotics

A high-quality, multi-strain spore- and/or soil-based probiotic supplement is very helpful for replanting beneficial bacteria post-antibiotics.

I generally recommend taking probiotics during and at least for three months after taking antibiotics (and yes, some probiotics do survive antibiotics, especially those in spore form).

However, taking probiotics without prebiotics would be like throwing seeds on concrete and expecting them to grow!

Prebiotics, like inulin, FOS (fructoligosaccharides), and fiber from various fruits and vegetables, provide the food for probiotics to grow, multiply, and thrive.

So check the labels of your supplements to make sure they also include prebiotic fiber.

I’ll share how to get more probiotics and prebiotics from the diet in subsequent sections.

2. Get Outside, Breathe In Fresh Air, And Get A Little Dirty

One fascinating thing we learned in our conversation with microbiome health expert Dr. Zach Bush (listen here) is that the great outdoors is our best source of beneficial bacteria.

Specifically, spending time breathing in fresh air from as many environments as possible—the woods, your backyard, your favorite walking place, grounding, etc.—infuses the body with millions of natural airborne probiotics, as well as other immune-enhancing substances.

For example, the volatile oils from trees, called phytoncides, have been shown to boost the function of natural killer immune cells.[12]

In addition, spending time in nature naturally reduces stress and anxiety and promotes healthy sleep, all of which benefit gut health and support immune function.

Finally, consider playing in the dirt with your kids or grandkids or planting a garden!

Research shows regular contact with dirt and soil provides multiple benefits for rebuilding the gut microbiome as well as boosting overall physical, mental, and emotional health and longevity.

The great outdoors is truly nature’s most effective probiotic!

3. Eat A Lot Of Plants

Want to know what to eat for better gut health? In a word, plants—and make sure they’re organic!

Plants grown naturally, such as in your own garden or on an organic or naturally raised farm, are rich in various types of fiber which is ultra-healing to the gut, and also contain natural microbes from the environment, which benefit our digestive tract.

Colorful plants also contain concentrated amounts of immune-boosting nutrients such as vitamins, minerals, trace minerals, antioxidants, essential fatty acids, prebiotics, and more.

How many plants should you eat after antibiotics?

Diversity and quantity are key, so aim for 30 different plants a week.

This includes fruits, veggies, whole grains, beans, legumes, herbs, and spices.

Some tips to make this easy include adding fruit and veggie smoothies, soups, stews, seaweed snacks, bowls, dips, pilafs, and salads.

And don’t forget to incorporate cultured plant foods, like kim chi, sauerkraut, real pickles, and cultured veggies which provide a natural source of probiotics. Aim for 1-2 servings per day.

For more inspiration, check out the following articles:

4. Get Morning Sunlight Into Your Eyes

Talk about simple: research has shown getting some unfiltered morning sunlight into your eyes benefits the gut microbiome and helps reset your sleep cycle.

One of the best ways to do this is to take a morning walk, which counts toward your daily exercise routine too!

Learn more in: Harnessing The Power Of Light: Exploring The Benefits Of Light Therapy

5. Sleep More Than Usual

Ample research (and commonsense advice from generations of mothers, healers, doctors, and grandmothers) has proven the connection between getting enough rest and more robust immunity.[13]

Sleep is also prime time for your body to detoxify and repair, which includes your gut.

Although 7.5-9 hours per night is generally recommended, I suggest getting at least 8.5 or more hours of sleep while you’re healing.

If you’re in a season of life where getting that much sleep at once is impossible (us moms and dads have all been there!), then prioritize naps and rest when you can.

Note, sometimes sickness can throw off our sleep cycle and make falling asleep difficult.

Gut health issues can also cause sleep disturbances.

If you’re struggling with sleep, make sure you get morning light, turn off screens two hours before bed, sleep in a very dark room, shut off your Wi-Fi at night, sleep in a cool room, and get regular exercise.

If this isn’t enough, talk to your healthcare practitioner about trying out the following herbs:[14][15][16][17][18][19]

Valerian
Ashwagandha
Passionflower
Bacopa
Chamomile

What About Melatonin Supplements?

Melatonin supplements can be useful to help reset your sleep cycle, but they shouldn’t be used long-term and must be used with caution. I also don’t recommend them for children.

Unfortunately, recent reports have shown that various brands contain much larger doses of melatonin than listed on labels.

See our article on trusted supplement companies and check with your doctor or healthcare practitioner for individual recommendations.

6. Include Resistant Starch In Your Diet

Resistant starch is a type of prebiotic fiber that resists digestion and ferments in the gut, where it feeds beneficial microbes.

Including more resistant starch in your diet is one of the best ways to rebuild gut health.

The best dietary sources of resistant starch and prebiotic fiber include:

Cooked and cooled potatoes (OK to reheat gently)
Cooked and cooled rice and other grains (OK to reheat gently)
Green plantains
Green bananas (I like to peel, cut, and freeze these to put into smoothies)
Jerusalem artichokes
Mushrooms
Asparagus
Leeks
Onions
Garlic
Beans
Chicory
Peas
Potato starch

Be sure to include at least two or three of these plants in your daily diet.

7. Address Your Stress & Cultivate A Healing Mindset

We hear a lot about the necessity of probiotics and diet for maintaining gut health.
However, the effects of stress, especially chronic stress, can be even more detrimental to gut health.

Several studies have shown that chronic stress increases intestinal permeability (aka: leaky gut) and promotes inflammation.[19][20]

One of the best ways to reduce stress is to address your mindset, aka your thoughts.

As we’ve discussed in previous posts, our thoughts become who we are---they’re that powerful.

So, if we are caught in a negative thought loop, our health will reflect that.

This is why all traditional systems of healing focus on the mind-body connection---you simply cannot attain and maintain physical health without optimal mental/emotional health, and vice versa.

Here are some tips to help create a more positive mindset:

Spend time with people who uplift you, not those who bring you down
Turn off the news! It’s not doing you any favors. If you must, check it on the computer once a day and be selective about what you read
Try a digital detox for a week
Put limits on screen time and keep your phone away from your body
Spend more time in nature. It provides an instant mood boost
Get enough sleep (see previous point)
Clean up your diet. Ingredients like excitotoxins, excess sugar, and ultra-processed foods have been linked to poor mental health
Pay attention to how social media affects you. Many people have transformed their mental/emotional health by quitting social media or greatly cutting back
Exercise every day. Even just a walk can do wonders
Prioritize social activity. Humans are social creatures and we need community as much as we need healthy food, water, and air
Make time to laugh!
Try tapping. Techniques like the Emotional Freedom Technique (which you can learn for free) teach you how to gently tap on acupuncture points to reduce stress, anxiety, and even unhealthy cravings or behaviors.
Meditate, pray, and practice mindfulness. Learning how to switch off your thoughts and use your mind as a tool (versus it controlling YOU) is essential to a healthy outlook on life

For more tips, see:

8. Lean On Immune-Boosting Herbs While You Heal Your Gut

Taking antibiotics takes your gut offline for several weeks or months, depending on the course and how sick you’ve been.

Since your gut makes up the majority of your immune system, this compromises your ability to fight off other infections (which is why people tend to get sick over and over after antibiotics).

Immune-boosting herbs are the ultimate allies during this time, as they will help bolster and support your entire immune system and benefit your gut.

Some excellent immune- and gut-supportive herbs to take long-term include:[21][22][23][24][25[26][27][28]

Turmeric
Fennel
Lemon balm
Ashwagandha
Tulsi
Elderberry
Medicinal mushrooms like chaga, shiitake, turkey tail, cordyceps, and reishi

Learn more about immune-boosting herbs in:

9. Swap Out Synthetic Cleaning Products For Safer Alternatives

It may seem counterintuitive to stop using harsh chemical cleaners when you’re trying to get well and avoid harmful germs.

However, these cleaning products contain multiple ingredients that disrupt microbiome health, depress immune function, and irritate the respiratory system.

Plus, like antibiotics, they wipe out all bacteria—beneficial and otherwise, and can lead to the proliferation of superbugs.

Related reading: Why Oversanitizing Does More Harm Than Good

Instead, we recommend choosing human-safe, biodegradable, plant- and mineral-based cleaners that remove germs, versus killing them.

Branch Basics, vinegar, peroxide, baking soda, and castile soap are all excellent options for a safe clean.

For natural sanitizing and disinfecting, we recommend 3% peroxide—either alone or used with vinegar (sprayed separately and stored in separate bottles), steam or dry steam cleaning.

Learn more in: Are Natural Cleaning Products Effective?

Let Branch Basics Help Your Create Healthier Home

We hope this article has laid to rest any fears you may have about how to restore and heal your gut after antibiotics.

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Branch Basics is safe for even the most sensitive individuals, including babies, toddlers, children, the immune-compromised, and pets.

It’s also super effective, naturally fragrance-free, 100% biodegradable, and affordable.

Learn all about our human-safe, eco-friendly, plant- and mineral-based refillable cleaning line here.

For more immune-boosting and natural sanitizing tips, check out the following articles:

References mentioned in this article:

Marilee Nelson

Marilee Nelson is an Environmental Toxins expert who has spent nearly 30 years advocating for the chemically-sensitive and chronically-ill. She is a Board Certified Nutritionist, Certified Bau-Biologist and Bau-Biology Inspector and specializes in Food As Medicine. She has helped thousands of families and individuals identify, heal and recover from toxic exposures and is on a mission to revolutionize the way American families view their health.

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How To Heal Your Gut & Rebuild Immunity After Antibiotics

By Marilee Nelson | 03/27/2025

Before We Start, Let’s Address The Elephant In The Room…

The Pros And Cons Of Taking Antibiotics

9 Natural Ways To Heal Your Gut After Antibiotics

1. Take Prebiotics And Probiotics

2. Get Outside, Breathe In Fresh Air, And Get A Little Dirty

3. Eat A Lot Of Plants

4. Get Morning Sunlight Into Your Eyes

5. Sleep More Than Usual

6. Include Resistant Starch In Your Diet

7. Address Your Stress & Cultivate A Healing Mindset

8. Lean On Immune-Boosting Herbs While You Heal Your Gut

9. Swap Out Synthetic Cleaning Products For Safer Alternatives

Let Branch Basics Help Your Create Healthier Home

References mentioned in this article:

Categories

Marilee Nelson

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How To Heal Your Gut & Rebuild Immunity After Antibiotics

By Marilee Nelson | 03/27/2025

Before We Start, Let’s Address The Elephant In The Room…

The Pros And Cons Of Taking Antibiotics

9 Natural Ways To Heal Your Gut After Antibiotics

1. Take Prebiotics And Probiotics

2. Get Outside, Breathe In Fresh Air, And Get A Little Dirty

3. Eat A Lot Of Plants

4. Get Morning Sunlight Into Your Eyes

5. Sleep More Than Usual

6. Include Resistant Starch In Your Diet

7. Address Your Stress & Cultivate A Healing Mindset

8. Lean On Immune-Boosting Herbs While You Heal Your Gut

9. Swap Out Synthetic Cleaning Products For Safer Alternatives

Let Branch Basics Help Your Create Healthier Home

References mentioned in this article:

Categories

Marilee Nelson

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Detox

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