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4 things you must do after a course of antibiotics

4 things you must do after a course of antibiotics

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Antibiotics are a touchy subject. There is a lot of overuse (you hear all the time about doctors prescribing them straight away, without even being sure what the issue is) and resistance is becoming a real problem.

4 things you must do after a course of antibiotics

Whilst I’d love to say I’d never take them, there are certain situations where antibiotics truly are a modern miracle. In fact, I took them not so long ago when I found out I was host to an unwelcome parasite. The problem with antibiotics, is that as well as killing off the infection, they also kill off all of the good bacteria in our gut.

With diminished good bacterial colonies in the gut, this can significantly reduce your immune system and mess with your hormone balance. But it doesn't have to be permanent. Here are some steps you can take to help your gut to repair as soon as you've finished the course of antibiotics.

1. Eat strict paleo

So perhaps you’re clean eating had lapsed slightly before your antibiotics – but now is the time to get back on the wagon. Ditch anything processed and eat real, whole foods, keeping sugar (from natural sources) and carbohydrates low whilst you’re healing.

2. Eat fermented foods everyday

Have some kombucha, sauerkraut, yoghurt or kimchi ready to go. Fermented foods will help to re-introduce probiotics to your gut – so make sure to mix up your fermented foods and eat them regularly. You can also look at probiotic supplements.

3. You've taken care of probiotics – don’t forget prebiotics

Soluble fibre such as that provided from root vegetables and peeled fruit is a great way to feed the good bacteria you need to re-establish.

4. Eat bone broth

Said to be able to resurrect the dead, bone broth is the ideal nourishment after your course of antibiotics. It will help support your liver and digestive system –so make sure you have a big batch ready to go.

Ok, so I've added a few more things…

5. Prioritise Sleep and Stress Management

Rest is one of the most overlooked components of recovery, but it’s absolutely essential after a course of antibiotics. Quality sleep allows your body to rebuild, repair tissues, and regulate immune function — all of which are vital when your gut is healing. Aim for at least 7 to 9 hours of uninterrupted sleep each night, and try to maintain a consistent bedtime. If you're struggling with sleep, reducing screen time before bed and using natural light during the day can help reset your circadian rhythm.

Equally important is managing stress. Chronic stress impacts the gut-brain axis and can hinder gut repair. Mindfulness practices such as meditation, yoga, breathing exercises, and even spending time in nature have been shown to reduce cortisol levels and support digestive health. The gut is incredibly sensitive to emotional and psychological stress, so make self-care a part of your post-antibiotic protocol.

6. Remove Gut Irritants

Even if you’re eating a strict paleo diet, now is a good time to take it a step further by eliminating any known gut irritants. This might mean avoiding eggs, nightshades, nuts, or high-FODMAP foods temporarily if you suspect sensitivity. These foods, while healthy for many, can provoke inflammation in a compromised gut. Focus on easy-to-digest meals like soft cooked vegetables, slow-cooked meats, and broths while you rebuild gut integrity.

Additionally, consider reducing caffeine and alcohol intake during your recovery. Both can irritate the gut lining, impair liver function, and disrupt your sleep — all of which slow down healing. Once you’ve re-established gut balance and overall wellness, you can reintroduce these elements mindfully, if they suit your lifestyle.

7. Support Your Liver

Your liver plays a huge role in detoxification — and after antibiotics, it’s likely working overtime. Supporting liver health can make a big difference in how quickly your body bounces back. Incorporate liver-friendly foods like leafy greens, beetroot, lemon, and dandelion tea. Cruciferous vegetables like broccoli and cauliflower also help increase your liver’s natural detoxification enzymes.

Supplements such as milk thistle, turmeric, and NAC (N-acetyl cysteine) can support liver regeneration and antioxidant status, but it’s always best to check with a healthcare provider before introducing new supplements, especially post-antibiotics. Your focus should be on supporting the liver gently and naturally through nourishing foods and hydration.

8. Reintroduce Movement – Gently

While your energy may be lower after illness and antibiotics, light movement can support lymphatic drainage, circulation, and digestion. Gentle walks, stretching, or even slow yoga flows are excellent ways to stimulate the body without over-exerting it. Movement also helps regulate stress, boost endorphins, and support healthy sleep — all essential during your recovery phase.

If you feel up to it, increase intensity gradually as your energy returns. Be mindful of how your body responds to exercise post-antibiotics, and don’t push through fatigue. Recovery is not a race, and overtraining can set you back rather than speed up the healing process.

9. Track Your Symptoms and Progress

Everyone’s microbiome is unique, so it’s a good idea to track your progress during recovery. You may want to keep a food and symptom journal for a few weeks to identify patterns. Pay attention to bloating, bowel movements, skin changes, mood, and energy levels — all of these are connected to gut health. If you’re noticing lingering symptoms such as fatigue, digestive issues, or new food sensitivities, it might be worth consulting with a functional medicine practitioner or naturopath to assess your gut more thoroughly.

There are also comprehensive stool tests available that can give insight into your current gut bacteria, the presence of pathogens, and levels of inflammation. While not always necessary after a single course of antibiotics, they can be helpful for those recovering from multiple rounds or long-term gut dysfunction.

10. Be Cautious with Future Use

Once you’ve been through the process of rebuilding your gut microbiome, you’ll likely be more mindful about when antibiotics are truly necessary. Not every cold or sore throat needs medication — in many cases, your body can heal with rest, hydration, and immune-supporting nutrition. The more we use antibiotics for minor issues, the greater the risk of antibiotic resistance, and the more damage we may be doing to our gut ecosystems.

If you do need antibiotics in the future, prepare your body ahead of time. Eat fermented foods, reduce sugar intake, and start a probiotic supplement alongside your medication (at a separate time of day to avoid immediate neutralisation). Continue the protocol of bone broth, prebiotics, and stress reduction throughout the course and for several weeks afterward.

Final Thoughts on Gut Recovery

While antibiotics can be life-saving when used appropriately, they come with consequences — particularly for your gut health. Fortunately, your body has an amazing capacity to heal when given the right support. By eating a wholefood paleo diet, prioritising rest, reducing stress, and nourishing your gut with probiotics, prebiotics, and broth, you can significantly reduce the disruption caused by antibiotics and bounce back stronger than before.

As always, stay in tune with your body. If something doesn’t feel right or symptoms persist, seek advice from a healthcare professional who understands gut health from a holistic perspective. Your microbiome is a living, responsive ecosystem — treat it well and it will return the favour.

What’s your approach to antibiotics? Have you taken many courses?

paleo diet gut health probotics-min

It’s not just about you…

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It may be a little strange to think of, but the body you inhabit isn't strictly your own. In fact, you’re sharing it with approximately 100 trillion bacteria that colonise your gut – your own unique army of micro-organisms. But it’s not as scary as it sounds, as these tiny creatures control your health in a variety of ways. Firstly, they extract energy from food; the greater the diversity of your gut bacteria, the more effectively you are able to digest nutrients. Gut bacteria break down carbohydrates, and prevent them from being stored as fat – hence the reason there is a direct correlation between insufficient gut bacteria and obesity. They also build your immune system, and are directly linked with your emotional health; restoring gut flora has been shown to boost mood and fight depression.

In the right conditions, you can live in harmony with your gut flora and co-exist very happily. Look after them, and in turn, they look after you. But, create a troublesome environment for them (through inflammation, stress, or antibiotic use amongst other things) and they will be compromised, and in turn, so will your health. Here are a few things you may wish to consider in order to care for your gut flora.

Paleo Diet and Gut Health – The Role of Probiotics

Consider a high quality probiotic

The first (and most obvious) thing you can do to support your healthy gut flora is to supplement with a high quality probiotic. This will help to repopulate your digestive tract with beneficial bacteria. Opt for a probiotic with a number of different strains of bacteria, and consider rotating your supplements over time to maintain greater diversity.

If you’re wondering how our ancestors maintained healthy gut flora long before probiotic supplements hit the shelves (or the shelves were even invented) then consider the point below!

Eat Organic Produce

Thousands of years ago, our ancestors’ gastrointestinal tracts would have been teeming with a huge diversity of bacteria, taken directly from the untouched soil in which their produce grew. They wouldn't have worried about washing their hands after digging for them, let alone washing the produce itself. Modern day agricultural methods and non-organic farming have seen our soils stripped of this bacteria; unfortunately, conventionally grown plants grow in soil that is virtually sterile. The solution? Buy organic, preferably local – and don’t worry about thoroughly washing scrubbing every vegetable. A bit of dirt will only be beneficial.

Eat Fermented Foods

Fermented foods play a large part in the diet of almost all traditional cultures, and would have further supplemented their gut biomes. Fermented foods like Kombucha, Sauerkraut and Kimchi are rich in beneficial bacteria; and they’re delicious, too. Consider making your own fermented foods, or if you have to buy them, make sure they are unpasteurised so the bacteria remains.

Eat food rich in prebiotics

Just like you, your gut bacteria need to be fed. Feed them the right foods, and they will thrive. Prebiotics are found in foods such as Chicory, Jerusalem Artichoke, Onions, Leeks and Garlic – and they stimulate and nourish the good bacteria in your gut.

Try resistant starch

Much like prebiotics, resistant starch provides optimum fuel for your gut bacteria. Resistant starch is starch that passes through the colon undigested, thus giving the bacteria an excellent food source. Paleo friendly sources of resistant starch include cooked and cooled tubers – especially arrowroot and cassava.

Avoid sugars and high GI Carbohydrates

On the other side of the coin, if you eat a diet high in sugar and other high GI carbohydrates, you are providing optimum fuel for the bad bacteria in your gut (such as Candida). Who knew there were any further reasons to give up the sugar and grains!?

Don’t Stress

Finally, the most important thing you can do to support your gut bacteria is to reduce the inflammation that makes their living environment hellish to live in. Along with a poor diet, stress causes excessive inflammation within the body. Take time to relax, exercise, perhaps meditate – so that your gut bacteria can do the same.

Focus on Sleep for a Healthier Gut

One often-overlooked element in gut health is sleep. Poor sleep disrupts circadian rhythms, which can negatively impact the diversity and balance of your microbiome. Research shows that even short-term sleep deprivation can alter gut bacteria composition — decreasing beneficial strains while encouraging the growth of those associated with inflammation and metabolic dysfunction.

If you're serious about cultivating a healthy gut, make restorative sleep a priority. Aim for 7–9 hours per night in a cool, dark room. Establish a relaxing bedtime routine, minimise screen exposure in the evenings, and try to go to bed and wake up at the same time each day. Even something as simple as a 10-minute walk after dinner can help regulate your circadian rhythm and support microbiome function.

Rethink Antibiotic Use (and Rebuild After)

While antibiotics have saved countless lives, they are indiscriminate in their effects — wiping out bad and good bacteria alike. Overuse of antibiotics can lead to long-term changes in gut flora, which may increase the risk of digestive issues, allergies, and even autoimmune conditions.

If you need to take antibiotics, support your recovery with a multifaceted strategy: reintroduce fermented foods slowly, continue your probiotic supplementation, and include prebiotic-rich meals to encourage the regrowth of beneficial bacteria. Avoid inflammatory foods like seed oils and processed snacks during this time to give your gut the best chance of full recovery.

Get Dirty (Literally)

In our overly sanitised world, we’ve lost some of the natural microbial exposure that previous generations took for granted. Children raised in ultra-clean environments may be more prone to allergies and immune dysregulation because their microbiomes didn’t get the chance to diversify and develop properly.

Spending time outdoors, gardening, walking barefoot on natural ground, and interacting with animals can expose you to helpful environmental microbes that contribute to your overall gut health. You don’t need to live on a farm to get these benefits — even regular contact with houseplants and fresh air can make a difference.

Chew Thoroughly and Eat Mindfully

Your gut health doesn’t begin in your stomach — it starts in your mouth. Proper chewing stimulates digestive enzymes and signals the body to begin the breakdown and assimilation of nutrients. Eating quickly or while distracted can reduce digestive efficiency and leave food less processed by the time it hits your intestines — which can impact how gut bacteria respond.

Take your time when eating. Sit down, avoid screens, and chew each bite thoroughly. This simple habit can reduce bloating, enhance nutrient absorption, and support your microbiome by ensuring food is properly digested before reaching the gut.

Hydration Supports a Thriving Microbiome

Staying hydrated helps maintain the mucosal lining of the intestines, which is a key barrier between your internal environment and the outside world. A healthy gut lining keeps bacteria where they belong — inside the digestive tract — and reduces the risk of leaky gut syndrome.

While plain filtered water is ideal, you can also include mineral-rich beverages like herbal teas, bone broth, and coconut water (in moderation). Avoid sugary soft drinks, fruit juices, and flavoured waters filled with artificial sweeteners, as these can contribute to bacterial imbalance and feed the wrong strains.

The Gut-Brain Axis: Support Mental Health Through Microbes

It’s not just digestion — your gut plays a massive role in mental health too. The gut-brain axis is a two-way communication network between your digestive tract and central nervous system, largely mediated by the vagus nerve and supported by healthy gut bacteria. An imbalance in gut flora can lead to mood disorders, anxiety, and even brain fog.

By nurturing your microbiome with whole foods, reducing inflammatory triggers, and addressing stress, you also support your emotional resilience. Many people report feeling calmer and more focused after improving their gut health, and emerging research backs this up. Your gut really is your “second brain.”

Eat a Variety of Whole Foods

Gut diversity thrives on food diversity. A common trap in modern eating — even in healthy diets — is falling into routine and eating the same few vegetables or proteins repeatedly. Instead, aim to include a wide range of colours, textures, and flavours in your meals each week.

This doesn't mean you need dozens of ingredients per meal — just rotate your produce choices regularly. Include different herbs, spices, and cuts of meat. Think of each new food as a new microbial input — variety truly is the spice of gut life.

Final Thoughts on Gut Health the Paleo Way

Supporting your gut flora isn’t about quick fixes — it’s a lifelong relationship built on consistent choices. Luckily, the Paleo lifestyle already aligns beautifully with what your microbiome needs: nutrient-dense foods, reduced inflammation, time in nature, and minimal exposure to processed ingredients and synthetic chemicals.

Instead of obsessing over one probiotic brand or chasing the next gut health trend, focus on the basics: quality sleep, diverse organic food, regular movement, and stress reduction. These foundations, when maintained consistently, do far more for your gut than any single supplement ever could.

🦠 How has your digestion or energy changed since prioritising gut health? Share your experience in the comments — and let’s continue learning from one another.