When Should I Take My Probiotics?

Kerry Beeson BSc (Nut. Med.) Nutritional Therapist

It’s no surprise that the most frequently asked questions when it comes to probiotics are usually about how to take them, we all want to make sure that we’re able to get the best out of our supplements. In this article we’ll answer all your questions on when to take probiotics:

confused woman
Wondering when you should take your probiotic?

Should I take probiotics on an empty stomach?

The concern here is that bacteria are delicate by nature, and that they may not survive stomach acid. Taking probiotics at a certain time of day (when stomach acidity may be more neutral) could help you to ensure the highest survival rates of your probiotic. Confusingly though, different healthcare professionals and probiotic manufacturers, have different guidelines about when is best to take these supplements! So let's try to clarify a few things.

First of all, let's look at the logic behind having probiotics on an empty stomach, advocated by some. Seeing as acid is stimulated by consumption of food, it is thought that taking probiotics on an empty stomach (mainly first thing in the morning) is better because there is less residual acid in the stomach. However, it’s also important to note that there is a lag time (up to 30 minutes) between when food is eaten and when acid is released into the stomach. As a nutritionist, I like to recommend that clients take their supplements with a meal, as the food helps to buffer the effects of stomach acid; it may also help to facilitate the passage of the probiotics through the stomach, and ensures that they are well mixed with the stomach contents as they pass into the small intestines.

With that being said, there are hundreds of probiotic strains available in the market, and different products may need to be administered at a specific time of the day for a reason. Take Saccharomyces boulardii for example; this is a strain that can be taken at any point in the day, with or without a meal and alongside antibiotics. That’s because it is very robust, so this recommendation might not apply to all probiotic strains. To note, most other probiotic supplements should be taken 1-2 hours away from this type of medication. Healthcare professionals can read more about Saccharomyces boulardii on the Probiotics Database.

We often get asked if you can take a probiotic before bed, well, some probiotic supplements that contain prebiotics could lead to initial bloating and gas, so these products might be best taken before bed. To learn more about prebiotics, read our article: What are prebiotics?.

Probiotic strains and research

There are other factors that matter more than whether to take probiotics morning or night, or whether we can take probiotics on an empty stomach or not. For example, of greater concern would be checking that you have the best specific probiotic supplements for your needs. Not all probiotics have the same health benefit as they all have different properties, so it's best to use specific probiotic strains to target specific health conditions. Don’t forget to also make sure these strains have lots of clinical trials to back up their efficacy! To learn more, read our article: Are all types (strains) of friendly bacteria the same?

Many gold standard clinical trials involving the use of probiotics don’t specify the time of the day the supplements were administered and it’s not a strictly controlled factor, which indicates that the researchers do not see it as a limitation. But, it still brings up the question of "when is the best time to take probiotics?"

Should I take a probiotic every day?

It may be prudent to supplement with a probiotic every day, especially if you are looking to help support certain conditions or maintain beneficial bacteria in the gut. But what time is best to take it? A 2017 clinical trial, published in the World Journal of Gastroenterology, was the first of its kind to explore this topic.

The study aimed to assess if the time the probiotics were administered affected their ability to colonise in the gut and provide health benefits by modifying the composition of the gut flora1.

The study involved 20 participants split into two groups of 10. They were all given the same amount of a probiotic supplement containing Bifidobacterium longum BB536 and Lactobacillus rhamnosus HN001; however, the first group took the supplement 30 minutes before their breakfast, and the other group had the supplement 30 minutes after breakfast.

They found that the ability of these strains to reach the intestine, colonise and provide beneficial health effects were not significantly affected by the time the probiotic supplements were administered. Both strains were seen to have a positive impact on the microbiome, as there was also an overall reduction in the levels of potentially harmful bacteria and an increase in beneficial bacteria in both groups.

Healthcare professionals can read more about Lactobacillus rhamnosus HN001 on the Probiotics Database.

Best time of day to take probiotics

  • The most important thing is to make sure you’re taking the best probiotic strain for your current health concerns or goals!
  • Generally, the best time of day to take probiotics is with breakfast, or just after.
  • It's equally important to take probiotics at a convenient time for you so you don’t forget.
  • Different probiotic strains behave differently. Some, such as Saccharomyces boulardii can be taken at any time of day, with or without food.

Check out the following links for further reading:

Probiotic Myths...BUSTED
Are all types (strains) of friendly bacteria the same?


  1. M. Toscano, R. De Grandi, L. Stronati, E. De Vecchi and L. Drago, "Effect of Lactobacillus rhamnosus HN001 and Bifidobacterium longum BB536 on the healthy gut microbiota composition at phyla and species level: A preliminary study," World Journal of Gastroenterology, vol. 23, no. 15, pp. 2696-2704 , 2017.
  2. Tompkins et al. (2011) The impact of meals on a probiotic during transit through a model of the human upper gastrointestinal tract. Beneficial Microbes; 2, 4: 295-303.