Can Probiotics Make You Feel Worse Before Better?

If you’re reading this post then I’m guessing you’ve just started taking probiotics and you’re wondering if they can make you feel worse before better. Well, the short answer is yes, they can. While probiotic supplements help improve gut health, especially for those with irritable bowel syndrome or small intestinal bacterial overgrowth, some people do experience discomfort or adverse reactions when introducing new beneficial bacteria into their routine. So what’s going on? Let’s take a look at probiotic side effects and how long they might last.

A hand holding probiotics and vitamins


As usual, I’m going to preface this by saying that I’m not medical and if you’re really worried stop reading and go see a healthcare provider. I’m just a random blogger. Although, I’ve been where you are, so if you want someone to commiserate I can probably manage that.

Anywho back to probiotics.

How Do Probiotics Work?

To understand why probiotics can make you feel worse before feeling better, it helps to know what these live microorganisms actually do. For the uninitiated, probiotics are strains of live bacteria and yeasts that are beneficial for your health, particularly your digestive system. These are the good bacteria that help keep your gut ecosystem balanced and operating. Your intestines are a delicately balanced micro-society where trillions of bacterial residents work behind the scenes to keep you healthy. 

However, the gut can sometimes become imbalanced. A strong dose of antibiotic treatment or too much sugar and there goes the neighbourhood. Probiotic reinforcements like Lactobacillus and Bifidobacterium can help replenish the depleted population and restore order. Once deployed, they get to fortifying intestinal walls, synthesising vitamins, processing waste, and generally keeping your internal infrastructure running smoothly.

blue gut microbiome bacteria against a black background

These days you’ll find an overwhelming array of bacterial strains vying to recolonise your digestive tract promising flatter stomachs, better bowel movements, and a whole new you. However, probiotics won’t be ready for battle right after you ingest them. They need time to settle in, do a little decorating and unpack the boxes. During this period, they’ll multiply and join forces with the existing army in your digestive tract, the normal gut flora.

After that, the probiotics will crowd out the bad bacteria while producing compounds that nourish your intestinal cells and improve your digestive problems.

Different Probiotic Strains

Different probiotic strains offer different health benefits. For instance, lactobacillus helveticus (Nothing to do with the font- it’s the Latin name for Swiss: you’ll find it in Swiss cheese) can help support your brain function, while lactobacillus rhamnosus is known for its positive effects on the gut-brain axis. On the other hand, lactobacillus plantarum is beneficial for maintaining a healthy balance of gut bacteria in the GI tract. 

​Can Probiotics Make You Feel Worse?

it’s not actually uncommon for probiotics to make you feel worse before you start to feel better. (As long as you do start to feel better). Shuffling in a whole new cast of characters tends to create temporary chaos wherever they land. This can cause all sorts of unpleasant side effects, often referred to as die-off symptoms or Herxheimer reaction, as the body experiences a sudden increase in the toxins released by the dying harmful bacteria. 

Symptoms include:

  • Abdominal pain, gas, bloating and all the things you’re essentially trying to cure
  • Brain fog and cravings 
  • Increased histamine levels leading to symptoms like a runny nose or skin rashes
  • Irregular bowel movements as your gut flora rebalances and your shiny new bacteria promote a healthy gut microbiome
  • If you take yeast-based probiotics, you might also experience increased thirst and constipation.

So, yes, probiotics can cause you to feel slightly worse before it gets better. You might want to start gradually.

However, these symptoms, are usually temporary and short-lived. This will vary depending on your gut health and the specific strains of probiotics that you go for. Generally, die-off symptoms are considered a sign that the probiotics are actively working within your system but if you’re in any doubt, or have severe or persistent symptoms, seek medical advice. Everyone’s body reacts differently, and what might be a good idea for one person may not have the same positive effect on another.

loose probiotic tablets on a white table beside a green leaf

And of course, there are those infuriatingly lucky people that don’t react to probiotics at all. It’s all down to your gut’s unique community dynamics.  

​Just remember to monitor how your body responds to the new probiotic regimen. Over time, the discomfort should subside, and you may start to notice improvements in your gut health and well-being.

Other Possible Side Effects of Probiotics


Certain probiotic-rich foods, like kimchi and sauerkraut, contain high levels of biogenic amines. It’s rare, but these amines might trigger headaches and migraines in some people, so if you’re prone to that kind of thing go easy.


Yeast-based probiotics, also known as saccharomyces boulardii, can potentially protect your gut flora when taking antibiotics and help replenish the good bacteria afterwards. However, they’re not a good idea if you have a yeast allergy, so watch out for that.

Allergic Reactions and Filler Content in Probiotics

When you’re choosing a probiotic supplement, make sure to check the label for other ingredients. You may find a host of fillers alongside your chosen probiotic strains.  This can include:

  • – Cellulose, which is used as a binding and coating agent
  • – Gelatin, used in capsules
  • – Stearic acid and magnesium stearate, used as lubricants
  • – Silicon dioxide, used as an anti-caking agent and flow enhancer
  • – Microcrystalline cellulose, used as a filler

While fillers are generally safe, you might be sensitive to certain ingredients like carrageenan, potassium sorbate, titanium dioxide, or artificial colours and flavours. For that reason, it’s a good idea to try and find one that keeps the extras to a minimum. 

A brown probiotic bottle with a red nouri label tipping tablets into an open palm above a plate with a fried egg on it

When selecting a probiotic supplement, look for one that:

  • – Contains billions of CFUs per dose, ideally at least 30 billion if not more
  • – Has multiple probiotic strains, especially Lactobacillus and Bifidobacterium species
  • – Uses minimal fillers and excipients, and avoids ingredients like lactose, cornstarch, artificial colours and flavours
  • – Has the manufacturing date or expiration date clearly listed

Enteric-coated capsules can help protect the probiotics as they pass through the stomach. If that doesn’t work for you, there are loads of powders, gummies, suppositories and liquid drops that you can try instead.

Are Probiotics Safe?

Absolutely. Probiotic bacteria already exist in your body, meaning probiotic foods and supplements are generally safe. Unlike pathogenic bacteria, The good bacteria that are probiotics won’t cause disease. While allergic reactions and die-off symptoms are possible, If you already eat fermented foods like kimchi, sauerkraut and kefir without any discomfort then you’re probably on the safe side. 

​Probiotics and Me

I started taking probiotics when I was first diagnosed with IBS (which a surgeon has recently told me is ‘not a thing’, but more on that later). It made a huge difference. My life was a mess of trying to keep up. I was caring for my parents, trying to promote myself and running around the capital for auditions. I didn’t get booked, but I did come away with a lot of bad bacteria as a consolation prize for the stress, processed food on the go and questionable sushi. 

If it had been just bloating and feeling sluggish I would have probably carried on as before. My body, however, had other ideas. It was so bad I had to stop and take some time to get well. That included learning everything I could about gut health and naturally, I went all in with a scorched earth approach.

a close up of green salad leaves

Out went the high fodmap foods, refined sugars, and other likely dietary irritants. It was quite the elimination diet and I don’t recommend not eating to anyone. Don’t be like me, play it safe and get some medical guidance to help you find the culprits. I started daily probiotic supplements, and frankly huge amounts of probiotic-rich yoghurt and kefir. It was pretty bad there for a while as my old microbial tenants protested their eviction. Ultimately though, patience and doubling down on my regimen prevailed and probiotics did start to make me feel better.

 Not every probiotic initiation needs to be as fraught as mine, of course. But hopefully, this story illustrates that even when probiotics can make your gut issues feel worse, perseverance through temporary symptoms is often worth it. A rejuvenated microbiome and healthier gut can definitely emerge on the other side.


So, can probiotics make you feel worse before better?

The answer is yes. Things can get a little worse in the first few weeks. You might experience some mild digestive symptoms, including bloating, gas, and diarrhoea.

But this shouldn’t last more than a few weeks, and your body will start adjusting to the beneficial bacteria. If the symptoms persist for more than that, you might be suffering from an unrelated condition or an allergy to one of the ingredients. If that happens, stop the probiotic supplementation, and contact your doctor. Remember, you’re not bothering anyone – your well-being matters. So don’t hesitate to consult with the experts.

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