When it comes to probiotics — their effectiveness, different types and brands, foods vs. supplements — everybody seems to have a different opinion. Even the deceivingly simple question, “When is the best time to take a probiotic?” is up for debate.
You may have heard the advice to only take probiotics with food or without food; in the morning or at night; combined with prebiotics or alone — the options are many and often confusing.
In this article, we’ll discuss when to take probiotics, when you should add probiotics into your gut-healing protocol, what probiotics are good for, and clear up several myths around probiotics and their uses.
Take Probiotics on Your Schedule
Here’s the bottom line: The best time to take a probiotic is whenever you can take it consistently, and taking it doesn’t interfere with living your life.
There’s lots of advice online saying that probiotics should be taken with food or without, in the morning or before bed, as a powder or in a capsule, all in the name of optimizing their effects. The truth is that these factors don’t matter all that much. The much more important thing is that you remember to take probiotics consistently (without worrying too much if you miss a day or two), whatever that means for you.
You absolutely can and should:
- Take probiotics any time of day, whenever it’s most convenient for you.
- Take probiotics with or without food: You can experiment to see if one feels better for you than the other.
- Take probiotics when you take antibiotics: Research shows that taking probiotics alongside antibiotics tends to make antibiotic treatment more effective [1, 2, 3, 4].
When to Add Probiotics Into Your Gut Health Protocol
In terms of adding probiotics into your treatment plan in general, we do recommend starting probiotic therapy after you’ve optimized your diet, the foundation for good gut health. This is step two in my Healthy Gut, Healthy You gut-healing protocol. Starting with a healthy diet helps calm inflammation, eliminate trigger foods that may be causing symptoms, and prioritizes nutrient-dense foods that also feed your microbiome.
Once your therapeutic diet is in place for a few weeks, the microbiome is primed to work with probiotics and begin rebalancing the microbial community in your gut.
We typically recommend the Paleo diet for most people to start on, since it is the least restrictive while providing lots of key nutrients and meal options.
It’s also best to add probiotics before introducing most other kinds of gut supports (such as antimicrobials). Probiotics and diet alone can be very powerful when it comes to improving your gut and overall health, and you might find that further treatments are not necessary.
Why Should You Take Probiotic Supplements?
Probiotics have a multitude of health benefits, and not just for your gut health. Scientific study has connected probiotics to improvement in numerous health conditions, from the immune system to thyroid health to mood regulation.
Probiotics Improve Digestive Health
There is a lot of high-quality evidence for probiotics having positive effects on the digestive system, including:
- Increasing diversity (the types of probiotic strains) of good bacteria in the microbiome 
- Increasing growth (the quantity of probiotic strains) of good bacteria in the microbiome 
- Reducing inflammation in the gut 
- Repairing leaky gut, or damage to the intestinal lining [8, 9, 10]
- Fighting pathogens, harmful microbes that can cause inflammation and release toxins in the digestive tract [11, 12, 13]
- Improving symptoms of irritable bowel syndrome (IBS), such as constipation and bloating [14, 15]
- Improving symptoms of IBD, Crohn’s disease, and ulcerative colitis [16, 17, 18]
- Treating bacterial overgrowth in the small intestine (SIBO), contrary to the idea that you shouldn’t take probiotics because you already have too much bacteria to begin with [19, 20, 21].
Probiotics Improve Other Areas of Health and Wellbeing
The benefits of probiotics don’t stop at gut health. Research shows that probiotics have beneficial effects on a number of other health conditions and systems of the body, including:
- Better sleep [22, 23, 24]
- Improved mental health and reductions in anxiety and depression [25, 26, 27]
- Thyroid health 
- Immune system regulation [29, 30]
- Brain fog and cognitive health 
- Alzheimer’s disease [32, 33]
- Fibromyalgia 
- Autoimmune diseases, including Type 1 diabetes [35, 36]
- Allergies, both food and seasonal [37, 38]
This is just scratching the surface of the benefits of probiotic supplements.
What About Eating Probiotic Foods?
Probiotic foods, like yogurt, kefir, kimchi, sauerkraut, and other fermented foods are great sources of beneficial bacteria. But, unless you’re eating many servings of these foods every day, they don’t add up to the benefits of a high-quality probiotic supplement with many more CFUs (colony forming units) per serving.
Still, probiotic foods and prebiotics -— foods that provide fuel for probiotic bacteria in the gut — are excellent to incorporate into your diet on a regular basis. The trick to adding these foods to your diet, especially if you have preexisting digestive issues, is to start low and slow, allow your body to adjust to the change, and then add another new food only after you have tolerated the last one.
If you find that you can’t tolerate a certain probiotic food — cow’s milk kefir, for example — simply put it aside for now and try coming back to it once you’ve made some further progress with your gut healing.
For as long as probiotic supplements have been around, there has also been confusion around their effectiveness and how to optimize them. Let’s address some of these probiotic myths.
Myth #1: Stomach Acid Kills Probiotics, So Taking Them Is Ineffective
Sometimes, there’s a grain of truth hiding in a myth. In this case, stomach acid definitely can kill off some probiotic bacteria when you take a probiotic supplement, possibly up to 60% . However, that doesn’t mean that the probiotics aren’t effective.
Firstly, some strains — like Saccharomyces boulardii, B. animalis, and L. johnsonii — aren’t bothered by the acidic environment of the stomach at all. They are able to pass through into the intestines totally intact and alive. But here’s the really fascinating thing: Studies show that even non-viable probiotics, strains that have died off on their journey through the digestive system, still have health benefits [40, 41]. This underlines the fact that we’re still learning about how probiotics work within the human digestive system.
Ultimately, we have hundreds of well-designed clinical trials showing that probiotics are beneficial for many aspects of human health. This is the science that we should pay attention to, rather than mechanistic studies that can’t fully replicate the environment within the digestive tract.
Myth #2: Probiotics Work Better When You Take Them in the Morning/at Night
The arguments for taking probiotics at a certain time of day, usually first thing in the morning or before bed, go something like this:
- Argument #1: Probiotics should be taken in the morning to set up good digestion for the day.
- Argument #2: Probiotics should be taken at night before bed to help the digestive system reset during sleep (away from food intake).
The reality is that these arguments are simply conjecture. Human clinical trials simply show that probiotics work, regardless of when they are taken. Plus, we know that the effects of probiotics are cumulative, meaning that they build up over time. Taking a probiotic at night because you want to improve your digestion and, therefore, sleep quality, for example, doesn’t make sense. Probiotics don’t work the same way that a sleeping pill would; the effects aren’t instantaneous.
What we’re looking for is sustainable change over a period of weeks to months. In that framework, the most important thing is to take your probiotic consistently in a schedule that works for you.
Myth #3: Taking Probiotics With Antibiotics Cancels Out Their Effects
Another myth that has persisted over the years is that taking probiotics at the same time as antibiotics is wasteful, since the antibiotics would kill off the probiotics. Another argument is that the probiotics will make the antibiotics less effective. But this couldn’t be further from the truth. Research shows that taking probiotics alongside antibiotics actually makes antibiotic treatment more effective [1, 2, 3].
Probiotics can also help reduce side effects that often come with taking a round of antibiotics, like antibiotic-associated diarrhea . Probiotic therapy is even recommended alongside antibiotics in difficult cases of C. difficile infection [4, 43].
Myth #4: Probiotics Are More Effective With/Without Food
You’ll find many recommendations online around whether or not to take your probiotics with food. Some advise:
- Only take probiotics away from meals
- Only take probiotics with meals
- Take probiotics 20 minutes before eating.
Again, the research doesn’t line up with the recommendation to take probiotics either with or without food. We have one study that shows that probiotics have better survivability when taken along with a source of healthy fats. But this study was done in a model digestive system, not in human clinical trials, so it doesn’t really replicate how probiotics operate when you take them .
Use Your Best Judgement on When to Take Probiotics
You are welcome to experiment with taking your probiotics with or without food, in the morning or evening, mixed into a beverage or in capsules. You may find that tying your probiotics to a certain time of day or consuming them with a meal helps you remember to take them. Or if you are sensitive to supplements in general, taking probiotics with food may act as a helpful buffer to your digestive system.
Whatever works for you is “the best” way to take probiotics. Fortunately, taking a probiotic is not like taking a medication, so there aren’t any set rules about when or how to take them. Use your best judgement and find what works for you.
When Is the Best Time to Take a Probiotic? When It’s Convenient for You
Probiotics are a remarkable therapy for gut health, immune system regulation, brain and cognitive support, and many other facets of your health and wellness.
While a few outlying studies may show benefits to taking your probiotics with food or before a meal, the large majority of studies simply specify that the benefits of probiotics come with taking them consistently over time. One general rule to be mindful of is to get your optimal diet in place before starting probiotic therapy. But other than that, there’s no need to stress about the best time to take a probiotic — just follow a schedule that works for you.
If you would like the support of an experienced practitioner to figure out how probiotics can support you on your health journey, reach out to us at the Ruscio Institute for Functional Medicine and book a consultation.