Is There Really a Best Time to Take Probiotics?

Grace Clark-Hibbs

February 25, 2021

No dietary supplement has gotten more publicity over the past decade than the probiotic. But if I’m being completely honest, most of the information out there is conflicting, confusing, or flat out misleading.

This article aims to clear up some of the confusion and help you sort through what’s true, what’s maybe true (AKA what needs more research), and what’s just plain false. By the end of the article you will be able to answer the question, “is there really a best time to take probiotics?” and so much more!

But first, let’s start with the basics…

What Are Probiotics?


Probiotics are formally defined as, “foods/[products] that contain live cultures of specific strains of microorganism in sufficient numbers to alter the microflora of the gastrointestinal [GI] tract, ideally to exert beneficial health effects.” (1)

Basically, probiotics are live bacteria strains that, when consumed, have the ability to change the makeup of the gut microbiome and (hopefully) improve aspects of our health. Today there are even probiotic beauty products and creams meant to improve certain skin conditions by altering the microbiome of the skin. (2, 3)

This has lead to the definition of probiotics being expanded to, “live microorganisms that confer a health benefit on the host when administered in adequate amounts.” (4)

Now, I know what you’re thinking. How can bacteria in our gut and on our skin be a good thing?

Although the common understanding is that bacteria = germs and germs = bad, not all bacteria are harmful. In fact, some types of bacteria are beneficial, and even essential, to our every day bodily functions. These functions include digestion, immunity, and vitamin production. (2)

Having a diverse and balanced microbiome throughout the body is an important aspect of optimal health. Unfortunately, our microbiomes are sensitive and can be easily pushed out of balance by our diets, environment, and use of chemicals (such as antibacterial products).

This is referred to as dysbiosis and can lead to a wide variety of health conditions, including small intestine bacterial overgrowth (SIBO), small intestine fungal overgrowth (SIFO)/candida, IBS, and more.

Probiotic sources: food vs supplement

Probiotics can be found naturally in fermented foods, such as kefir (a yogurt drink), sauerkraut, kimchi, miso, and tempeh (the last two are fermented soy products).

Fermented foods contain live microorganisms and have been shown to provide health benefits, such as anti-oxidant, anti-microbial, anti-fungal, anti-inflammatory, and anti-diabetic activity. (5, 6)

That being said, many people don’t eat these foods on a regular basis (especially those following a Western diet). So the question becomes, is taking probiotics in pill, or supplement, form equally beneficial to our health?

And the answer is…’it can be’. Allow me to explain.

The fermented foods listed above are often expensive or unavailable in your neighborhood grocery store. Or maybe you’ve tried kimchi before and it’s just not for you. These are both valid reasons for not being able to include these foods in your diet.

Therefore, it is an acceptable alternative to take a probiotic supplement when it’s not an option to get them from food. That being said, not all probiotic supplements are created equal.

Since supplements are not required to go through the same rigorous approval process that medications are, the consumer must verify for themselves that the company and product are reputable and are actually providing what they say they are providing.

However, the Food and Drug Administration (FDA) is currently working on two improvements to the process for approving dietary supplements, which will dramatically improve the consumers ability to identify which products are right for them. (7)

  1. Dietary supplements will be required to list the quantity of live microbial ingredients by a standard unit (i.e. colony forming units – CFU).
  2. They can not contain inactive or dead organisms.

In the meantime, we need to do our own investigating and the information below should help you narrow your focus.

What Makes a Good Probiotic Supplement?

The strain

There are only a few strains of probiotics that have demonstrated positive health effects through peer-reviewed research. Look for a brand with one or more of the following strains when picking a probiotic supplement: (8)

  1. Lactobacillus & Bifidobacterium predominated blends
  2. Saccharomyces Boulardii
  3. Bacillus species

The bacteria count/dosing

Standard recommendations say that there should be at least 1 billion CFUs available in each dose, however a study from 2015 suggests a dosage of 5 billion CFUs per day or greater was significantly more effective than a lower dose. (9)

In short, more is generally not going to hurt you, but it’s always important to consult your healthcare professional before starting a new supplement.

The condition you’re trying to manage

Probiotics have been shown to help a variety of conditions. The conditions with the most amount of research to support the use of probiotics include:

It’s important to point out that it is difficult to perform the “gold standard” of research (i.e. randomized-controlled trials) on supplements in humans. This means that many of these studies were conducted on animals or in a lab, have a small sample size and/or have a study population that lacks diversity. Therefore, we cannot definitively say probiotics will improve symptoms in all people.

Other conditions that may improve with the use of probiotics (but require additional research) include:

  • Bad breath (or halitosis) (24, 25)
  • Skin health (2)
  • Dental health (26)
  • Irritable Bowel Disease (IBD) (27, 28, 29)

So, What IS the Best Time to Take Probiotics?

A quick Google search of this question will show you that everyone is saying something different. Some say probiotics are best taken on an empty stomach, others say it’s best to take them right before bed, and there are even others that suggest taking them right after meals. It’s difficult to know what advice to follow.

I’m going to do my best to break it down for you.

The big question nutrition researchers are trying to answer is, what is best for bacterial survival? The stomach is extremely acidic because it’s designed to kill off harmful microorganisms and to start digestion. After the food leaves the stomach it will enter the first part of the small intestine, which is highly basic.

Both of these environments are harsh and make it difficult for living organisms to survive. If the probiotics can make it through these sections of the gastrointestinal (GI) tract they have a much higher chance of having a positive impact on the gut.

What does the research say?

One study showed that the type of food or drink taken with the probiotic can actually help protect the microorganisms from the harsh environments of the stomach and upper small intestine. (30)

This study suggests that taking the probiotic 30 minutes before eating or at the same time as food with a little bit of fat (i.e. 1% milk) had the best results. The worst outcomes were seen when the probiotic was taken after eating or with plain apple juice or water. (30)

Another study showed improvement of the gut microbiome in people after using probiotics for one month. The interesting thing to note here is that these improvements occurred regardless of whether the probiotics were taken before or after eating food. (31)

As you can see, probiotic research is still relatively young. This means that more research needs to take place in order to fully answer when the best time to take probiotics is.

In the meantime, current research supports taking probiotics with 1% milk or low-full fat yogurt and about 30 minutes before eating. For best results, I recommend taking the probiotic at the same time everyday.

Are Probiotics Safe?

Only minor side effects have been reported in healthy individuals. These include gas and bloating and should subside over time. If your gut symptoms don’t improve, or they get worse, you may be suffering from SIBO. Consult with your healthcare professional about how to test for this.

Probiotics are not recommended for people who have impaired immune symptoms or are critically ill. Always consult with your healthcare professional before starting a new supplement and don’t forget to discuss potential interactions with current medications.

Probiotic Best Practice Tips

Although there is no consensus about when the best time to take probiotics is, there is evidence to support certain best practices. See my 4 best practice tips and recommendations for choosing, taking and storing your probiotic:

  1. Choose a probiotic strain/s that has been studied and shown to be beneficial for the use you are wanting it for. Find one with organisms from all three major strains:
    • Lactobacillus & Bifidobacterium predominated blends
    • Saccharomyces Boulardii
    • Bacillus species
  2. Choose a high-quality brand:
    • Multiple strains working together
    • The end product has been studied and shown to have beneficial effects
    • The dose is at least 1 billion CFUs
  3. Consistency overtime is more important than a specific time of day
  4. Store it properly:
    • Check the label
    • These are living organisms and often need to be stored in the fridge
4 best practice tips & recommendations for taking probiotics

Final Thoughts

We still have a lot to learn about how probiotics work and how to maximize their benefits. What we do know is that they can change the microbial makeup of our bodies. They also have the potential to improve more than just our guts.

Finding the absolute best time to take probiotics is complex and will require more time and research. It appears to be more important to take the probiotics consistently and with a little bit of fat rather than at a specific time of day.

One more thing, no one has all the answers. So, if you come across a resource that claims they do, be skeptical.

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Grace sitting

Hi, I’m Grace! A registered dietitian and gut health expert based in Portland, OR, where I live with my husband and our orange tabby, Tony. As someone who has struggled with my own severe, chronic, and painful bloat and constipation for over 15 years, I understand what it’s like not to get the answers you’re looking for from conventional medical support. So I decided to take matters into my own hands and figure out what was going on for myself using a functional nutrition approach and identifying my root causes. This approach was a game changer for me and now I’m on a mission to share it with every other woman experiencing embarrassing gut issues. You are not alone!

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