Swapping out fries for broccoli, soda for sparkling water, and fast food for home-cooked meals seems like a straightforward path to a healthier you.

But the truth is, switching to a wholesome diet doesn’t always feel good right away for some. 

When you break away from a diet high in sugars and fatty foods, your body goes through an adjustment period. Some people transition with no issues.

Others find themselves dealing with loose stools and frequent bathroom trips.

Experiencing this might leave you confused. After all, weren’t you supposed to feel better after cleaning up your diet?

The answer is typically yes. But, the road to reaping the full benefits of a healthy diet can come with a few digestive hiccups along the way.

3 Reasons Your Healthy Diet Might Cause Stomach Issues

Understanding the potential triggers for stomach pain is the first step in addressing this common health problem. Here are three reasons why your new and improved diet might not be sitting well:

1. Changes in diet can affect the gut microbiome

The trillions of microbes living in your gut form the complex ecosystem called the microbiome. When you change your diet, you also change your microbiome. 

It’s important to remember that changes to the gut microbiome don’t happen overnight. The process is gradual. When shifting to a healthier diet, your gut ecosystem undergoes a period of adaptation. 

This transition may lead to symptoms like diarrhea as your body starts to host a new balance of microorganisms.

Over time, as you consistently feed your body with nutritious foods, these symptoms should decrease.

This change mirrors the body’s natural response to diet changes. It shows the need for patience and persistence when moving to a healthier lifestyle.

The foods we eat play a big role. They can influence the growth of certain bacterial strains, boosting gut health.

Fermented foods are a good example. They are rich in probiotics, which can help the gut. 

Kefir and sauerkraut are great examples. They boost the population of good bacteria like Lactobacilli. These bacteria aid in digestion and strengthen the immune system.

Additionally, garlic and onions contain prebiotics.

Prebiotics feed and support the growth of helpful gut bacteria. These foods encourage the presence of Bifidobacteria and can help in reducing harmful bacteria in the gut. 

This can lead to positive long-term changes like more good gut bacteria. But, you might have digestive discomfort when you first change your diet, including diarrhea, as your gut bacteria adjust.

2. Increased fiber intake can cause temporary digestive upset

Fiber is a key part of a healthy diet. It helps you feel full and supports digestive health.

The downside is that boosting your fiber intake, especially insoluble fiber found in whole grains, can cause gas, bloating, cramping, or alter bowel movements. 

So, while fiber is great (and essential) for your health, your stomach might need time to adjust to having more of it.

A tool like MyFitnessPal can help you record your daily fiber intake.

You should aim to increase it by 5g each day until you meet the daily recommendation, which is 25 g/day for women and 38 g/day for men. 

3. Increased water intake can affect bowel movements

When eating healthier, you’re often encouraged to boost your water consumption.

Hydration is critical for overall health. But ramping up your water intake too quickly can lead to more frequent bowel movements. 

Excess water can speed up food’s transit through your digestive tract, resulting in loose stools. It’s like putting your digestion on the fast track, which your gut might not be used to.

Fun fact: In 2023, MyFitnessPal members logged over 5B cups of water

Less Common Triggers for Stomach Issues

If symptoms are persistent, consider an elimination or FODMAP diet to pinpoint the source of your stomach pain. 

FODMAPs (fermentable oligosaccharides, disaccharides, monosaccharides, and polyols) are a group of carbohydrates that can be difficult to digest.

Many healthy foods, such as fruits, vegetables, and grains, are high in FODMAPs. 

These foods are essential to a balanced diet. Unfortunately, consuming them in large quantities can cause significant gastrointestinal distress, specifically in people sensitive to FODMAPs.

The good news is that only about 10% of the population has to worry about this happening.

If you consider going this route, you should speak with your healthcare provider.  

Tips for Creating a Healthy Diet

You don’t want to give up on living healthy just because of short-term stomach issues. Fortunately, tools like MyFitnessPal can help you track what you eat to see if you can pinpoint the issue.  

If you are experiencing diarrhea, here are some tips from MyFitnessPal scientific advisor and nutrition scientist Dr. Nicola Guess:

• Stay hydrated
• Avoid sports or energy drinks
• Track your fiber intake, and don’t go overboard
• Avoid alcohol and caffeine
• Check your food ingredients lists for polyols, which are sweeteners that can cause diarrhea (common examples include sorbitol, xylitol, and mannitol)
• Be kind to yourself

Experiencing diarrhea when starting a new diet might dampen your enthusiasm. But it’s a common roadblock to a healthier you.

The body often needs time to adapt to new eating habits, so some discomfort during this transition is not unusual. 

But, persistence and a mindful approach to dietary changes can help you overcome these hurdles. And you can benefit from the positive long-term effects of healthier eating habits. 

If these stomach issues persist or severely affect your quality of life, consult a medical professional. Remember, your health is a marathon, not a sprint.

Gradual changes will help you cross the finish line of wellness with resilience and a happy gut.

Originally published 6/1/2020; Updated 5/10/2024