Side Effects of Probiotics and How to take them Safely?

by Raychel Agramon, RN, MPM, February 07, 2020

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Probiotics are good bacteria that can enhance digestion and improve skin complexion – many studies have proven these facts. But as with any other supplement, it comes with some potential side effects. This should not stop you from starting a probiotic regimen though. Worry not as this article can help you learn more about the possible side effects that come with probiotic intake – and what you can do to avoid them.


  • Bloating and Gas 
  • If you are new to the probiotic life, then you might find yourself suffering from the unpleasant side effects of bloating and gas. It’s not lovely, but come to think of it this way: your body is not YET used to the millions of good bacteria that you have just taken in. Bloating and gassing might be uncomfortable, but they are the body’s ways of adjusting to the colonies of good bacteria. 

    What You Need to Do: 

    • Exercise to get the ‘air’ out. 
    • Drink lots of water and avoid alcohol, as this will make you even gassier. 
    • Consume food products that fight the inflammatory process. Good examples include nuts, fatty fish, and green leafy vegetables. 
    • Take probiotic-rich food or supplements on an empty stomach. This will minimize the probiotic-food interactions that can lead to gas. 
    • Should the following tactics fail, take a digestive enzyme supplement. It can break food down more efficiently, thereby preventing the symptoms of gas and bloating.

  • Diarrhea

    With bloating and gas comes another likely side effect of probiotic use: diarrhea. Similarly, this is the body’s way of adjusting to the good bacteria that are steadily overpowering the shady characters in the gut. Probiotics, after all, work by balancing the flora of the intestinal system. Give your stomach one to two weeks to become accustomed to the probiotic colonies – you will surely feel good right thereafter! 

    What You Need to Do: As it was mentioned, all you need to do is to give the system some time to fine-tune its workings. Take fermented food little by little so that your gut can adjust accordingly. If that doesn’t cut it, you can revert to supplements, which rarely cause diarrhea. Just make sure to take the capsule on an empty stomach for the best results.  

    side effects of probiotics

  • Constipation
  • Since probiotics primarily work on the gut, its side effects usually deal with the gastrointestinal system. One such manifestation, although rare, is constipation. Probiotics, after all, is said to relieve constipation.

    What You Need to Do: Constipation that occurs with probiotic use might mean that you are not getting enough water or fiber in your diet. Drink up and eat your fruits and vegetables! These diet changes can help improve your bowel movements in no time! 


  • Headaches
  • Do you find yourself chugging a Tylenol after eating some sauerkraut or kimchi? You can blame that on the antihistamine and tryptamine that are produced when fermented food is digested. These amines affect your nervous system by altering blood flow to your brain. The result? Pesky headaches. 

    Another reason that headaches occur is the fact that the good bacteria are slowly overpowering the bad ones. When these organisms die, they release toxins that can lead to headaches and other physical manifestations.

    What You Need to Do: Delicious fermented food can be hard to resist, but if you experience headaches often, it’s time to lower the amount you consume. A better alternative is to opt for supplements as they come with just the right amount of probiotics. 


  • Allergic Symptoms
  • Do you feel itchy or suffer from a runny nose after eating a serving of probiotic-rich food? This does not mean that you are allergic to probiotics outright. This usually occurs because of the bacteria’s ability to elevate the levels of histamine, a substance that plays a role in the inflammatory response.   

    What You Need to Do: If allergy-like symptoms occur every time you eat fermented food, you should consider cutting the servings or eliminating the products that make you feel this way. Always remember that there are a lot of options out there, including supplements that can give you the probiotics that you need (minus the itching and redness!)

  • Infection
  • Probiotics are more than safe to use, but as a precautionary measure, people with severe illness or compromised systems should avoid them. Those taking anti-fungal medications are advised to stay off probiotics until the infection has subsided. 

    What You Need to Do: Make sure to check with your doctor before starting a probiotic regimen, especially if you have an existing illness or condition. While probiotics are very beneficial, it’s unwise to start them without your physician’s go signal. 

    The side effects of probiotics are very minimal compared to what you get after taking antibiotics and other medications. They come with more benefits too, especially when it comes to intestinal and skin health. Remember: Probiotic side effects can be avoided as long as you follow the tips that were mentioned above.