Probiotics Detox Symptoms Explained (With Solutions)

Probiotics Detox Symptoms: Possible Causes, Side-Effects & Treatment Explained

Probiotics, or “good” bacteria, are known for being helpful to the digestive system. They are often taken to maintain gut health as well as to treat digestive conditions. Therefore, it might be surprising to hear that probiotics can actually cause some negative side effects as well.

There are a number of different symptoms that people can experience. And many of these are similar to the symptoms from detox dieting. If you are experiencing any unwanted side effects from your probiotics, don’t worry. This is just a sign that your probiotics are working and that your gut is responding to the new bacteria.

Chances are they won’t last long. However, if they are severe or long-lasting, do consult your doctor.

In this article we will dive into the possible symptoms probiotics can cause, why this happens, their similarities to detox symptoms, and what to do if you are experiencing them.

What are the side effects of probiotics?

So what are the side effects that probiotics can cause? There are a large variety of probiotics out there and the symptoms can vary depending on the type. But some of the common symptoms people can experience from probiotics are the following.

Gas and bloating

One of the most common reported symptoms caused by probiotics is a temporary increase in gas and bloating. (1) This usually happens within the first few days of introducing new probiotic supplements into your diet, especially in response to large quantities.

It can last up to a few weeks, but if it continues after this period, consult advice from a medical professional. Why does this happen? Well, as your gut is not used to the new bacteria it has been exposed to, there is a transition process happening within your body.

The bad bacteria in your gut is being replaced with the new “good” bacteria and this may cause flatulence, bloating and abdominal pain.

Digestive issues

Some people may also experience other digestive irregularities when introducing probiotics to their diet. Some research shows that yeast-based probiotics can cause constipation or an increase in thirst.

Allergic reactions

If you suffer from allergies or intolerances then you may be more likely to have an allergic reaction to probiotic supplements. Many supplements contain ingredients that can trigger reactions so make sure you read the ingredients thoroughly first.

Many probiotic supplements can contain the following ingredients so be aware if you have an allergy to any of these:

  • Dairy
  • Eggs
  • Soy
  • Yeast
  • Prebiotics like lactulose, inulin or oligosaccharides
  • Sugar
  • Lactose

If you do have an allergy to ingredients in a strain of probiotics, it is advisable to avoid these entirely. If you have a yeast allergy, choose bacteria-based probiotics instead of yeast-based ones. For lactose-intolerant individuals, studies show that up to 400mg is unlikely to trigger a reaction. (2)



Headaches are another common side effect you may experience when eating foods that naturally contain probiotics. This effect can be caused by amines, which are often found in probiotic-rich foods. (3)

These can impact the nervous system as well as blood flow which can trigger headaches or migraines.

However, research is still inconclusive about the extent of the effects. Some of the most typical Biogenic Amines (BAs) you may find are:

  • Histamine
  • Tyramine
  • Tryptamine
  • Phenylethylamine

Some foods that Biogenic Amines (BAs) can be found in are:

  • Kimchi
  • Yogurt
  • Sausages
  • Fermented vegetables
  • Cheese

If you find that these types of foods cause headaches, it may be preferable to take probiotic supplements instead.

Increased levels of histamines

Histamine is a Biogenic Amine that is released by the body when the immune system is fighting threats in the body. Some probiotics contain bacteria that can encourage the production of histamine in the digestive tract.

What happens when you have increased histamine levels? Your blood vessels undergo some changes by expanding and becoming more permeable. This allows more blood and immune cells to reach the affected area.

Normally any reactions to histamines are regulated in the body by a chemical called Diamine Oxidase (DAO).

However, some people who have a histamine intolerance, may experience symptoms similar to an allergic reaction. This could include itching, scratchy eyes, a runny nose or shortness of breath. (4)

If you have a histamine allergy, avoid histamine-rich foods and probiotics that encourage histamine production. These include Lactobacillus buchneri, Lactobacillus helveticus and Lactobacillus hilgardii.


The risk of developing an infection is very low for most people, however, for some people, the risk can be higher.

People at higher risk may be people who have a weaker immune system, people with underlying conditions or serious illness, or people who have recently had surgeries.

Studies show that the risk of infection from Lactobacilli bacteria, which is contained in some probiotics, represents 0.05% to 0.4% of cases. (5)

There are studies that suggest that those who suffer from acute pancreatitis should avoid probiotics altogether as they can trigger infectious complications. (6)

How long do symptoms last?

When you begin taking probiotics, you may experience symptoms within the first few days. These typically last up to two or three weeks but are unlikely to exceed this. If they do it is best to consult the advice of a doctor.

In general, most people may also find that it can take up to three weeks to significantly feel the positive effect of probiotics. This is because it takes some time to decrease the number of bad bacteria while increasing the good bacteria count.

Am I likely to get detox symptoms?

While most people are unlikely to get side effects from taking probiotics, some people are more likely to experience symptoms than others. Some people are particularly susceptible and may experience side effects and have a higher risk of infection. (7)

When are you more likely to be at risk?

  • If you have an unusually low immune system
  • If you have recently had surgery
  • If you have used a venous catheter
  • If you have a severe illness

Similarities to detox diet symptoms

There are many similarities to the symptoms caused by probiotics to those of detox dieting. Why is this? Well, both probiotics and detox dieting are ways to flush the system of toxins.

Increasing the number of good bacteria from probiotics, in a way, detoxifies the system of bad bacteria.

Detox dieting usually begins with fasting, aka abstaining from eating or drinking at all. It will often then move on to a highly restricted diet of water, juices from raw fruits and vegetables, and natural herbs and supplements.

As your body adjusts to the missing components they are used to, it may experience a number of symptoms. Your body may react particularly to the lack of certain types of food such as caffeine or sugar. The symptoms you can include:

  • Headaches
  • Fainting
  • Weakness
  • Hunger pangs
  • Dehydration

Some of these symptoms can mirror those caused by starting to take probiotics or probiotic supplements.

How to reduce symptoms?

If you are worried about the risks of probiotics there are some things you can do. A good way to lower the risk of getting symptoms is to introduce probiotics to your diet with caution.

Start by taking a small dosage of probiotics first and slowly increasing the dosage over the course of a few weeks. You will give your body time to get used to the probiotics slowly before building up to the full dosage.

How do you know if a probiotic is working?

How to tell if your probiotic is working? You will know when your probiotic is working once you start feeling the positive effects, which can range from improvements to digestion to clearer skin.

Probiotics help to rebalance the gut flora which helps to regulate digestive movements and strengthen the functions of your gut barrier. It can take a few weeks to start feeling the beneficial effects but these can include:

  • More regular bowel movements
  • Improved digestion
  • Relief from gas and bloating
  • Reduced risk of illness
  • Improved immune function
  • More energy
  • Lift in mood
  • Weight loss
  • Reduction in sugar cravings

Depending on the strain of probiotics and your body, you may start feeling different benefits at different times.

Benefits to digestion may only take one to two weeks to kick in, while other effects like mood enhancement or improved immune function can take up to eight weeks. If you are particularly sensitive you may even feel some of the benefits within just a few days.

If you feel any of the side effects above, that does not mean that your probiotics are not working. In fact, this can just be part of the natural process of balancing your gut flora and replacing bad bacteria with good bacteria. If symptoms persist, however, consult a medical professional.

Bottom line

For the most part, for healthy individuals, taking the right probiotics should bring positive improvements to your gut health and digestion as well as other benefits.

It is rare to experience many or severe side effects but it is possible for some people. Especially for those who are particularly susceptible or who have allergies or underlying health conditions.

The types of symptoms you might experience can be similar to those of detox dieting. While they are usually not a cause for concern, always proceed with caution. Avoid ingredients that could cause a reaction and consult a doctor if symptoms continue. 

To learn more about probiotics in complete detail, we recommend checking out our comprehensive guide here.

References –

1) Rao SSC, Rehman A, Yu S, Andino NMD, Brain fogginess, gas and bloating: a link between SIBO, probiotics and metabolic acidosis., retrieved from

2) Montalto M, Gallo A, Santoro L, D’Onofrio F, Curigliano V, Covino M, Cammarota G, Grieco A, Gasbarrini A, Gasbarrini G, Low-dose lactose in drugs neither increases breath hydrogen excretion nor causes gastrointestinal symptoms., retrieved from

3) Doeun D, Davaatseren M, Chung M, Biogenic amines in foods., retrieved from

4) Baste OC, Perez SS, Nogues MTV, Moratalla ML, Carou MDC, Histamine Intolerance: The Current State of the Art., retrieved from

5) Borriello SP, Hammes WP, Holzafel W, Marteau P, Schrezenmeir J, Vaara M, Valtonen V, Safety of Probiotics That Contain Lactobacilli or Bifidobacteria., retrieved from

6) Besselink MG, Santvoort HCV, Buskens E, Probiotic prophylaxis in predicted severe acute pancreatitis: a randomised, double-blind, placebo-controlled trial., retrieved from

7) Boyle RJ, Browne RMR, Tang MLK, Probiotic use in clinical practice: what are the risks?., retrieved from

Written by Hanna Greeman

Hanna is a professional writer who creates content across a wide range of topics. She has a special interest in medical and health writing.

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