When to Take Prebiotics for the Best Effects and How to Know if You Should Add Prebiotics to Your Routine

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Photo of a healthy young woman sitting In a chair touching a plant. Taking prebiotics can help support the good bacteria in your gut and reinforce overall health.

Prebiotics feed beneficial bacteria in the gut and keep the microbiota balanced. A supplement helps fill in the gaps where your diet may be lacking. The best time to take prebiotics is every day, at a consistent time that works for you.

The gut is an intricate, complex system that is integral to overall health. Taking care of it can be as simple as changing your diet or incorporating a prebiotic or probiotic supplement. However, the guidelines are often muddy.

Taking prebiotics supports microorganisms in the gut, resulting in health benefits impacting the immune system, digestive health, metabolism, mental health, and mineral absorption.

Although the benefits of prebiotics are clear, information on how to incorporate them is often confusing or contradictory.

You’re already doing yourself a favor if you decide to take a prebiotic at all.

The American diet is typically not a good source of prebiotics. In fact, it is estimated that only five percent of Americans meet the recommended daily intake of fiber. As a result, we’re increasingly susceptible to a long list of diseases and conditions as a result. A supplement fills in the gaps.

That being said, how you take a prebiotic is key to seeing the most impact on gut health. In this article, we’ll dive further into the best time to take prebiotic fiber and the health benefits that come from appropriate timing.

A healthy young woman drinking water in a gym. Taking prebiotic supplements at the same time every day with water helps make them the most effective.

When’s the Best Time to Take Prebiotics?

Prebiotics work best when they’re taken consistently. That means the best time to take them is whenever you can stick to taking it daily. Start by choosing a time that’s easiest to stick to.

If you suffer from digestive disorders like irritable bowel syndrome (IBS), Crohn’s, or any form of chronic digestive discomfort, you may need to experiment to avoid taking your prebiotic at a time that could cause discomfort.

If you already take a probiotic, even better!

As you supplement probiotic bacteria along with their prebiotic food source to support their growth it causes what is sometimes referred to as a synbiotic effect. This restores gut health and may help manage or even prevent certain conditions.

You can take your prebiotic around the same time that you take your probiotic, but you’ll want to space them out around 10 to 15 minutes. Otherwise, the two could interact too early, before they reach the large intestine which may lead to bloating.

It’s best to take your probiotic first, on an empty stomach.

A woman checks the time on her smart watch. Maintaining a regular schedule for taking prebiotics is key to making sure they are as effective as possible.

Should You Take Prebiotics at a Certain Time of Day?

In general, it’s okay to take prebiotics when you wake up or before you go to bed. Or really, any time of day that works for you. The most important thing is to take them daily. Here are some things that may factor into the best timing for you:

Stomach Acid: Our digestive systems lack the enzymes to break down prebiotic fiber, which means stomach acid doesn’t break them down or decrease absorption. Therefore, unlike probiotics, there is no need to time your prebiotics based on when your stomach is empty or full.

Medications: Since prebiotics pass through the digestive system without being absorbed, they could decrease absorption of certain medications. To be safe, it’s best to take prebiotics at least 2 hours before or after medications.

Digestive conditions: If you have a digestive condition like IBS, SIBO or FODMAP, you might prefer to take prebiotics before bed. Since the gut is at rest while you sleep, this helps to avoid any mild side effects like gas or diarrhea. Starting with a small dose helps as well.

Should You Take Prebiotics with Food?

The best way to take prebiotics is with a glass of water. Therefore, most people prefer to take them before a meal. It’s not necessary to take them on an empty stomach, but it depends on your preference.

Certain digestive conditions could determine how you time your prebiotics and meals. Remember, prebiotics are incredibly high in fiber. If you’re prone to uncomfortable symptoms like bloating, taking prebiotics with a meal could exacerbate these issues.

Since prebiotics travel through the digestive system unscathed, it’s not likely that food impacts the effects of prebiotics on probiotic gut bacteria such as Lactobacillus or Bifidobacterium.

In fact, prebiotics are commonly found in foods such as chicory root, leeks, legumes, and jerusalem artichoke, or in some fortified foods.

Signs You Should be Taking Prebiotics to Support Gut Health

Gut microbiota is composed of beneficial bacteria and bad bacteria. The balance of these bacteria influences intestinal health, which impacts the entire body. Prebiotics work to restore and maintain this balance.

Prebiotics are certain types of carbohydrates made up of nondigestible fibers like inulin and oligofructose. These fibers travel through the digestive system to the large intestine. There, they go through a process of fermentation.

The byproducts of this process feed beneficial, anaerobic bacteria. Feeding anaerobic bacteria is imperative to gut health, because these good bacteria can’t be taken in supplement form.

Fermentation also alters the pH in the gut to make the environment more favorable for healthy bacteria to flourish. This helps to restore balance and optimize probiotic function in the intestines.

Most people could benefit from taking prebiotics. Our diet is typically high in refined sugar and carbohydrates (especially refined and simple carbs like bread and pasta), which actually feeds harmful bacteria. Prebiotic foods include vegetables and high-fiber foods, which the American diet typically lacks.

Therefore, we recommend taking a prebiotic supplement for anyone who wants to optimize gut health. Even if you feel like your gut is fairly healthy, prebiotics provide an extra layer of support. This is important because so many factors influence gut health.

Stress, aging, poor diet, decline in overall health, and taking antibiotics are all factors that can disrupt homeostasis in the gut. The imbalance of bacteria can cause inflammation. Eventually, you’ll have noticeable signs of poor gut health such as:

  • Bloating
  • Cramping
  • Digestive irregularity (diarrhea and/or constipation)
  • Gas
  • Indigestion

Poor gut health isn’t isolated to the digestive system. In fact, gut health can impact nearly every system in the body. Some lesser known effects that stem from imbalance and inflammation in the gut include:

In other words, it’s very easy to have issues in the gut and not even realize it. Letting these issues continue over time can lead to malabsorption and chronic disease.

So, although the majority of this article focuses on the specific time of day to take a prebiotic, it’s also important to consider the when you might want to start taking prebiotics to either prevent or heal conditions that result from poor gut health.

A healthy man does a slam dunk while playing basketball. Proper nutrition and a balanced gut with prebiotics and probiotics can help people with an active and healthy lifestyle.

How Long Do Prebiotics Take to Work?

The longer you take prebiotics, the better. It takes time for probiotic bacteria to respond to prebiotic support. Continued support creates an environment that facilitates long-term health benefits.

Prebiotics enhance the gut environment to support probiotic growth and a healthy balance of bacteria. However, those changes happen at a cellular level, which takes time.

Some uncomfortable symptoms like constipation, diarrhea, and bloating could subside a few days after implementing a prebiotic and other dietary changes. You have to continue taking a prebiotic consistently to fully heal the gut and prevent symptoms from returning.


A healthy balance of gut microbiota is a significant part of overall health and preventing disease. Taking prebiotics is a simple, direct way to support healthy bacteria in the gut.

Consistency is key when you take prebiotics. Therefore, the best time to take prebiotics is whatever time allows you to take them daily. You can take them in combination with your probiotic supplement as well, but it’s best to space them apart.

Another important factor to consider is that not all prebiotic supplements work the same way. Omni-Logic is a line of precision prebiotics. Each prebiotic supplement has been carefully developed to feed anaerobic bacteria in the gut and combined with specific micronutrients. Each prebiotic formulation targets specific functions, such as immune support or healthy metabolism.

Don’t expect a quick fix when you incorporate prebiotic and probiotic supplements. It takes time for the conditions in the gut microbiome to change and for bacteria to grow. The longer you take these supplements, the better.

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