Gut Health

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Evidence Based

This article is based on scientific evidence, written by experts and fact checked by experts.

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This article contains scientific references. The numbers in the parentheses (1, 2, 3) are clickable links to peer-reviewed scientific papers.

When Is the Best Time to Take Probiotics?

Written by Dr. Michael Ruscio, DC on May 16, 2025

Written by Dr. Michael Ruscio, DC on May 16, 2025 — Reviewed by Hilary Watts

• Why Take Probiotics?|
• Probiotic Foods|
• Stomach Acid Concerns|
• With or Without Food?|
• Probiotics With Antibiotics|
• Best Probiotic Strains|
• A Probiotic Protocol|

If you’re taking probiotics to support your gut health, you’re already on the right track. But maybe you’ve wondered a lot about timing: Should I be taking these with food? On an empty stomach? Morning or night? Let’s clear things up with the simple truth:

The best time to take probiotics is whenever you’ll remember to take them. That’s it.

Other questions about how to take probiotics can be equally overwhelming, such as: Will my stomach acid wipe them out before they have a chance to help? Can I take them with antibiotics? Do I need a specific strain for my health condition?

Sure, there are a few theories about how to make probiotics “more effective,” but what actually matters most is consistency. Taking a high-quality product regularly is far more important than obsessing over the timing or other circumstances.

Why Should You Take Probiotics?

It turns out probiotics aren’t just about gut health. These powerful little microbes have been studied in hundreds of clinical trials—and their benefits extend well beyond digestion.

Research shows that probiotics can support:

• Digestive issues like irritable bowel syndrome (IBS) 1, ulcerative colitis (a type of IBD) 2, small intestinal bacterial overgrowth (SIBO) 3, and leaky gut 4
  
• Non-digestive issues like poor sleep 5, hormone imbalance 6, autoimmune conditions 7 8, and problems with mood and cognition
  

You might be thinking: How can one supplement help with so many different issues?

It All Comes Back to the Gut

Here’s the thing: Your gut is connected to nearly every system in your body—from your brain and immune system to your hormones and metabolism. That’s why probiotics can have such a wide-ranging impact.

In your digestive system, probiotics can:

• Increase the growth and diversity of good bacteria 9
• Fight off harmful microbes and their toxins 10 11
• Support microbiome recovery from gut imbalances 12
• Support your immune system 13
• Calm down inflammation 14
• Repair your gut lining (reducing leaky gut) 4

When your gut is in better shape, your whole body feels the difference. In fact, I wrote an entire book about this connection—Healthy Gut, Healthy You. You can also check out my other pieces that touch on the gut-thyroid connection and the gut-brain connection. But let’s see how these connections translate into tangible, body-wide benefits. 

Probiotics Improve Many Other Health Issues

Probiotics go beyond improving digestion. By improving your gut health, probiotics can benefit other parts of the body you might not expect. Research shows that probiotics can have a positive impact on: 

• Anxiety and depression 15
• Acne 16
• Bacterial vaginosis 17
• Nutrient deficiencies 18
• Lactose intolerance 19
• Libido (for depressed women) 20
• Polycystic ovary syndrome (PCOS) 21
• A common pregnancy infection called Group B streptococcus 22
• Rheumatoid arthritis 23
• Seasonal allergies 24

What About Foods Rich in Probiotics? 

Fermented foods like kimchi, sauerkraut, kefir, and yogurt are great natural sources of probiotics. If you’re already eating a lot of these and your gut is in good shape, you probably don’t need supplements.

But if you’re dealing with specific health concerns, or not eating a variety of probiotic-rich foods daily, a probiotic supplement can give you a more reliable dose of beneficial bacteria.

Here’s a helpful chart showing how much probiotic content is in common foods compared to a supplement capsule 25 26 27:

Bottom line: Fermented foods are great, but supplements pack a more potent punch.

Does Timing (Or Something Else) Matter When Taking Probiotics?

The internet is full of advice on when and how to take probiotics. Here, I’ll clear up some common questions about when to plan your daily probiotic dose, plus some bonus questions about the effects of stomach acid and antibiotics.

Should You Take Probiotics Before, With, After, or Away From Meals?

Some sources suggest taking probiotics before or with meals to help more bacteria survive 28. While this is technically true in models of digestive systems, there’s no clear evidence that it leads to better health results in humans.

The same study of a simulated digestive tract suggested that food (fat) might improve probiotic survival 28. But real-world studies don’t always require people to take probiotics with or without food, and they still show beneficial results.

Bottom line: Although you can take probiotics before, during, after, or away from your meals, there’s no need to stress over timing. What counts is taking them daily.

Should You Take Probiotics at Bedtime?

What about claims that taking probiotics at bedtime will improve sleep? Interesting idea, but probiotics don’t work like sleeping pills. Take them consistently and your sleep quality may improve over time, no matter what time of day you take them 29.

Bottom line: Take probiotics at a time—morning or night—that fits your routine.

Can Stomach Acid Make Probiotics Ineffective?

You may have heard that stomach acid kills probiotics—and that’s partly true. Some strains are vulnerable 30. But here’s what matters:

• Some strains, like Saccharomyces boulardii, Bifidobacterium animalis, and Lactobacillus johnsonii, aren’t affected at all 30.
• Studies done in test tubes or simulations don’t fully reflect what happens in real life.
• We have hundreds of human studies showing probiotics work—even if some bacteria don’t survive the journey.

Even more fascinating: Some non-living probiotics (that were killed by heat or acid) still offer health benefits 31 32 33! That’s how powerful the compounds in these microbes can be.

Bottom line: Don’t worry about stomach acid—probiotic supplements still work.

Can You Take Probiotics and Antibiotics Together?

Yes—and, oftentimes, you should.

Some people assume probiotics cancel out antibiotics, or vice versa, but research shows the opposite. Taking both together can actually help protect your good gut bacteria from the effects of the antibiotic. Additionally, probiotics can help the antibiotics do their job.

For example, in a massive meta-analysis (study of studies) including over 20,000 patients with H. pylori infections, those who took probiotics with antibiotics had better outcomes than those who took antibiotics alone 34.

This benefit also shows up in cases of SIBO and other gut infections.

Of course, you can always talk to your practitioner to make sure probiotics work with your treatment plan. I recommend bringing some of the newer research with you!

Bottom line: Probiotics and antibiotics work better together.

Do Certain Kinds of Probiotics Work Better for Specific Health Issues?

In my early years, I thought so. If a study showed that a certain strain helped constipation, I’d try it with constipated clients. But then another strain worked… and then another.I saw the same pattern with probiotics for mood problems, IBS, SIBO—you name it.

Eventually, I realized: Probiotics don’t need to be micromanaged. Nearly all probiotic strains offer similar benefits—by supporting gut health, reducing inflammation, and restoring balance.

Bottom line: You don’t need to get strain-specific, just choose a high-quality probiotic.

Try a Strategic Probiotic Protocol

Here’s something most supplement companies don’t tell you: nearly every probiotic can be grouped into three main categories:

• Lactobacillus & Bifidobacterium blends
• Saccharomyces boulardii
• Soil-based probiotics (Bacillus species)

Rather than cycling through random formulas or fixating on specific strains, you can take a more strategic approach by combining these three categories. In the clinic, we call this the Triple Therapy Probiotic approach. This method not only simplifies your supplement routine—it may actually enhance results.

Why Use Multiple Strains?

Research increasingly shows that multi-strain probiotic supplements can be more effective than single-strain products, especially for gut-related issues like IBS. A 2024 meta-analysis found that multi-strain probiotics may have stronger and more consistent benefits for some IBS symptoms, including abdominal pain and bloating, compared to single-strain formulas 35.

And it makes sense: The gut microbiome is a complex ecosystem. Using a combination of different probiotic strains may better mimic the diversity found in a healthy gut, offering a more comprehensive, synergistic effect.

My Clinical Experience

In working with thousands of patients, I’ve found that a three-category protocol—using multiple species from each of the main probiotic groups—is often the difference between seeing modest improvement and seeing real, transformative results. That’s why I formulated a probiotic powder stick that combines these for you (and is mixable into smoothies, elemental diet shakes, or even just water).

Bottom line: Instead of getting stuck trying to match a specific probiotic to a specific symptom, use a simplified, science-backed method. For a powerful, therapeutic approach, try my Triple Therapy Probiotic plan, which includes  representatives from each probiotic category.

Heal Your Gut with Probiotics

Take your probiotic supplements in whatever way is easiest for you. The benefits of taking probiotics at a specific time of day are likely minimal at best. You can take probiotics once or twice daily. Many of my clients find it convenient to take probiotics with water in the morning and at bedtime. Others prefer to take probiotic supplements with meals.  

Regardless of your motivation for taking probiotics, if symptoms don’t improve after a few months, that’s the time to reassess and consider deeper testing or treatments. If you’d like help from one of our experienced gut health clinicians at the Ruscio Institute for Functional Health, just reach out.

The Ruscio Institute has developed a range of high-quality formulations to help our clients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you. The information on DrRuscio.com is for educational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.