side effects of probiotics


5 (Potential) Side Effects of Probiotics

side effects of probiotics

Headaches, bloating and more - unfortunately taking probiotics can start out with some compromises.

You know them as the “good” bacteria that can help keep your gut healthy. So, are there any side effects of probiotics? The short answer is yes, because nobody’s perfect.

side effects of probiotics


So, here's our cheat sheet of the potential side effects of probiotics that you might encounter within the first couple of weeks of taking them.

What are the Potential Side Effects of Probiotics? 

1. Headaches

When protein-rich foods are fermented, they can produce biogenic amines like antihistamine and tryptamine.[2]

Some studies suggest that these amines can affect your central nervous system and either increase or decrease blood flow, which can cause headaches or migraines.[3]

How to Manage It: Get your probiotics in a supplement form (the way we like ‘em), instead of from fermented food.

Try our best-selling Trust Your Gut Daily Essential Probiotic Capsules with 16 Billion gut-friendly probiotic bacteria and 6 scientifically researched bacterial strains. 


2. Allergy Symptoms

If you develop allergy-like symptoms after you start taking probiotics, don’t stress. It doesn’t necessarily mean you’re allergic to them—you might just be sensitive to histamines.

In some people, certain strains of bacteria can increase histamine levels in the GI tract, so the body reacts the same way it would to an allergen.[4] Too much histamine, and you might end up with a runny nose, itchy eyes or shortness of breath.

How to Manage It: If you’re overly sensitive to histamines, avoid probiotics that come from fermented foods like yogurt, kimchi, and kombucha. Go ahead and experiment with other strains to find one that works for you.

3. Diarrhea

Ah, the irony. One of the potential side effects of probiotics really can be quite crappy.

Although probiotics can actually help with chronic diarrhea, you might find that your poop isn’t quite right after starting them, and that’s OK.[5] Your body should sort itself out within a week or two and you’ll be back to regular programming.

How to Manage It: Try taking your supplements on an empty stomach to help mitigate the risk of diarrhea. And remember to drink lots of water!


4/5. Bloating and Gas

You knew we would end up here. Yes, if you’re experiencing some gastrointestinal issues after taking your probiotics you’re not alone.

This phenomenon is a little something called the Herxheimer Reaction. Definitely not as scary as the name sounds. You can read more about it here, but essentially it means your gut is working overtime getting used to the influx of new bacteria, and things are gonna get gassy. Sorry.

How to Manage It: Drink lots of water. Eat anti-inflammatory foods. Avoid alcohol. Get your sweat on. Dry brush your body. Say goodbye to your skinny jeans for a bit, and embrace that stretchy pant life.


The moral of the story here: Sometimes diarrhea means good things are happening. Stick with your probiotics until your body finds its groove and you’ll be glad you did.


Check out our Gut Health range for premium, scientifically researched probiotics that will make your gut happy and healthy along with other array of health benefits:

  • Trust Your Gut Daily Essential Capsules - a daily probiotic + prebiotic support to maintain a healthy and happy gut
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  • Trust Your Gut Powder - Organic certified and plant-based probiotic + prebiotic powder with 20 Billion probiotics per serving and 6 different gut-friendly bacterial strains. It comes in delicious Raspberry Apple or Lavender Lemonade flavors that are completely natural and sugar-free
  • Trust Your Gut Pixie Sticks for Adults - probiotic + prebiotic powder that melts in your mouth like candy! A delicious, completely natural and sugar-free way to keep your gut healthy and support your immune system
  • Trust Your Gut Pixie Sticks for Kids - probiotic + prebiotic powder that melts in your mouth like candy! A delicious, sugar-free and fun way to support your kids' immune and gut health. Designed for kids aged 4 and above


Too Long, Didn’t Read (TLDR)

Probiotics can sometimes cause more of the symptoms they are meant to treat in the initial weeks of taking them. By sticking with them your body will regulate and these side effects will pass.

Here's how to manage the top associated symptoms. 

 Headaches & Allergy Symptoms

How to help: If you’re sensitive to histamines, avoid probiotics that come from protein-rich, fermented foods and stick with a supplement form of probiotics.


How to help: Try taking your supplements on an empty stomach and drink lots of water.

Bloating & Gas

How to help: Drink extra water, eat anti-inflammatory foods (hello, turmeric), avoid inflammatory foods (goodbye, sugar, and alcohol), get moving, dry brush your body, and a temporary break from skinny jeans.