Probiotics are often recommended to support gut health, but many people wonder whether when you take them matters just as much as what you take. With so many probiotic strains, formulations, and instructions on the label, it’s not always clear when probiotics are most effective.
The short answer is that timing can matter, but not in the same way for everyone. The best time to take probiotics depends on factors like the specific strain, whether the supplement is taken with food, and what you’re hoping to support, whether that’s digestion, immune health, or recovery after antibiotics.
So when is the best time to take a probiotic? Should probiotics be taken in the morning or at night? And does taking them on an empty stomach really make a difference?
Below, we’ll break down what the research says about probiotic timing, how different strains behave in the digestive tract, and practical guidance clinicians often use to help people get the most benefit from probiotic supplements. As with most aspects of gut health, a personalized approach matters.
What are probiotics?
The International Scientific Association for Probiotics and Prebiotics defines probiotics as live microorganisms that offer a health benefit when consumed in the right amounts. Think of probiotics as gut-friendly bacteria found in food, drinks and supplements that are the same — or similar — to microorganisms that already live in the body.
There are many different kinds of probiotics, or species of beneficial bacteria, and each acts on the body in different ways, according to the National Center for Complementary and Integrative Health (NCCIH).
The probiotic species Lactobacillis, for example, can encourage your brain to produce more gamma-aminobutyric acid (GABA), a neurotransmitter that can help manage anxiety or depression, according to Stephanie Wallman, D.O., a former physician at Parsley Health in New York City.
Meanwhile, Bifidobacterium promotes the creation of butyrate, “which is essentially the food that our colon cells use for energy,” Dr. Wallman says. Butyrate can also regulate your body’s response to insulin, thereby helping you maintain a healthy blood sugar level, she adds.
What Are The Benefits of Taking Probiotics?
There are many great reasons to add a probiotic supplement to a healthy diet. Depending on the person and the type(s) of bacteria involved, taking probiotics, either as dietary supplements or through eating probiotic-rich foods, like yogurt and fermented foods, may help:
Research shows probiotics may also help treat digestive disorders like irritable bowel syndrome (IBS), and even aid with fat loss. But knowing when to take your probiotics is key to getting the most out of them.
The best time to take probiotics
“The best time to take a probiotic is on an empty stomach,” Dr. Wallman says. For most people, that means taking a probiotic first thing in the morning (at least an hour before a meal, Dr. Wallman advises), or right before you go to sleep. Leave the probiotic by your bed so you don’t forget.
However, this can vary depending on the probiotic. Some are better accompanied by specific foods that can improve a probiotic's change of survival in the digestive tract:
- Healthy fats
- Oatmeal
- Low-fat milk
To discover if a probiotic should be taken on an empty stomach or with a light meal, read the product's instructions. Be sure to also check the dosage, as that can affect what time is best to take your probiotic. Some research suggests it’s best to take a probiotic with, or just before a meal. Why? Fat helps keep the stomach less acidic, which ensures more bacteria from the probiotic supplements can survive long enough to make it to the large intestine.
Similarly, spore-based probiotics are better to take with foods. “Because they are in their spore form, they are not affected by the harsh acidic environment that comes with eating meals and they use the food to ‘hitchhike’ down to the large intestine,” explains Dr. Wallman. Studies have shown that they perform better when taken with food.
And if you’re on antibiotics, don’t make the mistake of taking your antibiotics and probiotics at the same time. Otherwise, you risk having all that “good bacteria” killed off by your antibiotic treatment. However, it can be helpful to take a probiotic while on an antibiotic to support healthy bacteria colonization in the gut—as long as the two aren’t taken concurrently. Dr. Wallman advises waiting at least two hours after taking your antibiotics to pop your probiotic. If you’re on any medication that says to “avoid food” with, like thyroid medication, keep your probiotic away from those meds as well to prevent interfering with optimal absorption, she says. Probiotics should also be taken away from antifungal medications such as clotrimazole, ketoconazole, or nystatin).
Where you get your probiotics from also matters
Aside from when you take your probiotic, it’s quality will also affect how much good bacteria makes it to your large intestine. “High-quality producers will put higher amounts of probiotics in their capsules to guarantee that the amount of CFUs advertised on the bottle is in each tablet for the length of its shelf life,” Dr. Wallman says. And higher-quality strains also have a longer shelf life, she adds.
If you’re using probiotics for a specific health condition, talk to your doctor about finding the right probiotic supplement for you.
Otherwise, find a high-quality broad spectrum probiotic supplement. Unlike spore-based probiotics, broad spectrum probiotics are usually made up of at least three different kinds of bacteria (ex. Saccharomyces and Bacillus). “Your gut microbiome is diverse, so it’s a good idea for your probiotic to be as well when using it for general health and wellbeing,” Dr. Wallman says.
Do probiotics need to be refrigerated?
In general, probiotic bacteria are naturally sensitive to heat and moisture, both of which can kill the specialized organisms and render them ineffective. This is why certain probiotic supplements require refrigeration and will include clear instructions from the manufacturer regarding storage and ideal temperature to maintain effectiveness. Luckily, since the best time to take many probiotics is on an empty stomach and your stomach is likely empty right after you wake up or before you go to bed, it’s also an easy time to access a refrigerator.
However, not all probiotics are in need of refrigeration. In fact, freeze-dried organisms—such as those found in our Parsley Health probiotic—are shelf-stable, giving them significantly longer shelf-lives than their live probiotic counterparts. Freeze-drying helps to stabilize the probiotics and allows for large amounts of bacteria to be concentrated into a smaller volume, increasing the final product’s potency and amount of CFUs.
When purchasing a probiotic, be sure to read the label closely. If your probiotic requires refrigeration, ensure your retailer has kept it refrigerated or if ordering by mail, that it’s shipped quickly with appropriate packaging and limited exposure to heat and moisture. Freeze-dried probiotics are much more resistant to extreme temperature shifts—such as the cold temperatures that can be experienced when being shipped in an airplane—so they can withstand air travel or shipment in hotter climates.
Before you purchase a probiotic, check with your doctor to ensure you receive a variety that’s best supports your gut health. Once purchased, be sure to follow the manufacturer’s recommendations for dosage and storage and if in doubt, refrigerate.
Key Takeaways On When To Take Probiotics
Probiotic supplements are effective, easy ways to boost your gut health, especially since it's difficult to get enough probiotics from diet alone. When taking a probiotic supplement, it's best to read the product's instructions to determine if it's best on an empty stomach or with food. If you're wondering what probiptic supplement is right for you, check with your doctor.
