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Why Your Stomach Hurts After Eating (& 5 Ways to Fix It)

Written by Dr. Michael Ruscio, DC on May 17, 2025

Written by Dr. Michael Ruscio, DC on May 17, 2025 — Reviewed by Hilary Watts

• The Modern Gut|
• Why Your Stomach Hurts After Eating|
• 5 Treatments|

You’ve just finished a meal that should be good for you—maybe a fiber-rich salad and a piece of fruit, or some beans and greens. But instead of feeling nourished, you feel off. Maybe you have bloat, stomach pain, heartburn, or acid reflux. 

And the most confusing part? These are healthy foods. You’re not overeating. You’re doing what you’ve been told to do. So why do you feel worse?

The answer may surprise you. It’s often not the food itself that’s the problem—it’s how your body is reacting to it.

In this article, we’ll break down what’s actually going on when your stomach hurts after eating—not just the what, but the why. And more importantly, I’ll share five clinically-backed treatments that don’t just mask your symptoms, they help fix the root cause.

Let’s start with where this dysfunction begins—in your gut ecosystem.

The Modern Gut: A Microbial Collapse

For most of human history, we lived close to the earth. We farmed, foraged, ate fermented foods, and drank from rivers and wells. Every bite and every breath trained our immune systems to recognize and tolerate microbes.

But modern life has changed that.

We chlorinated our water, industrialized our food systems, and refrigerated everything 1 2. We’ve stopped relying on foraged and fermented foods. We’ve overused antibiotics. And gradually, the rich, diverse ecosystem in our gut has started to decline.

A fascinating 2021 study of 2,000-year-old stool samples found that our distant ancestors had much more diverse gut ecosystems that contained gut microbes not found in modern humans. It seems that a significant number of gut microbes native to the human ecosystem have gone extinct 3.

Why does that matter?

Because diversity in your gut microbiome helps keep everything in balance. When diversity drops, certain gut bacteria can overgrow, move into the wrong places, and trigger inflammation. The result? A gut that overreacts to harmless food—like a smoke alarm going off when there’s no fire.

Let’s look at the three main reasons your body might be reacting this way.

Why Does My Stomach Hurt After Eating?

The following are four common causes of bloating, pain, stomach ache, and other post-meal symptoms:

1. SIBO: Bacteria in the Wrong Place

Normally, most of your gut bacteria live in your large intestine, where they help break down fiber and produce anti-inflammatory compounds like butyrate.

But when too many of those bacteria move into your small intestine, where nutrient absorption happens, they start fermenting food too early. That fermentation produces gases like hydrogen, methane, or hydrogen sulfide in a part of the gut that wasn’t built to handle it.

This gas stretches the intestinal walls, activates pain receptors, and sends “danger” signals up to your brain. When bacteria take over the small intestine, it’s called small intestinal bacterial overgrowth (SIBO). 

SIBO symptoms can include:

• Abdominal pressure and distension
• Cramping
• Slower digestion
• Heightened pain sensitivity (also called visceral hypersensitivity) 

A review of studies found that up to 30% of people with irritable bowel syndrome (IBS) have SIBO, often without knowing it 4. 

SIBO is one of the most overlooked causes of food sensitivity. The food isn’t the issue—it’s where and how it’s being digested.

2. Immune Overactivation and Mast Cells

Your gut houses the largest collection of immune cells in your body. Among them are mast cells, which sit just under the intestinal lining, acting like guards for the immune system.

When mast cells detect stress signals—like gut barrier breakdown or bacterial fragments—they release powerful chemicals like:

• Histamine (causes bloating and pain)
• Tryptase (amplifies inflammation)
• Prostaglandins (sustain immune activity)

If these chemicals are released too often or in the wrong context, your gut becomes hypersensitive. When your gut is hypersensitive, even a normal amount of gas can feel painful. A healthy meal might trigger bloating and even anxiety.

In a very small clinical trial based on mouse studies, IBS patients who followed a low FODMAP diet for 4 weeks saw significant drops in histamine and tryptase levels 5, meaning fewer immune reactions and fewer symptoms. 

3. Nervous System Dysregulation: Gut-Brain Misfires

The vagus nerve is the main communication line between your gut and brain. And most of that communication actually flows upward—from your gut to your brain 6.

When your gut is inflamed, overstretched, or filled with immune signals, your brain receives the message loud and clear: Something is wrong. In response, it may:

• Slow down digestion (causing bloating and constipation)
• Amplify pain signals
• Increase anxiety or tiredness

An observational (survey) study found that nearly 40% of adults met the criteria for a disorder of gut-brain interactions in 2023 7.

This is why treating the gut alone sometimes isn’t enough. You have to restore the nervous system communication loop.

4. Slow Gut Motility Leading to Reflux and Constipation

Motility is how the muscles of the digestive tract move food from the mouth to and through the intestines. Slow motility means that things aren’t moving along as they should. Because motility is controlled by the nervous system, sometimes nervous system dysregulation (mentioned above in Cause #3) is at the root of slow motility. 

Other times, imbalanced gut bacteria can lead to slow motility. As you may have guessed, slow motility can manifest as constipation, and constipation can cause nausea, bloating, and stomach discomfort. 

Slow motility (in the stomach and esophagus) is implicated in gastrointestinal reflux disease (GERD) and heartburn, both of which can make your stomach hurt after eating.  

5 Science-Backed Treatments That Target the Root Cause

I want to emphasize that these aren’t just general wellness tips. These are clinically tested strategies we use every day in the clinic to help people like you heal their digestive health.

1. Low FODMAP Diet: Calm the Gut Fast

FODMAPs are fermentable carbs found in foods like onions, garlic, beans, and apples. In a healthy gut, they’re no big deal. But for someone struggling with SIBO or gut inflammation, they can act like fuel for gas and bloating.

By removing FODMAPs temporarily, most people can:

• Reduce gas and pressure
• Calm immune reactions
• Give your gut a chance to reset

A meta-analysis (study of studies) found that a low FODMAP diet outperformed traditional dietary advice in reducing pain, bloating, and irregular bowel movements 8.

Protocol

With our clients, we typically have them do the following low FODMAP diet protocol:

• Elimination phase: 4–6 weeks
• Reintroduction: 8–12 weeks, in phases
• Long-term personalization based on tolerance

Low FODMAP is not a forever diet. Think of it more like a short-term tool for long-term success. Research shows most people can reintroduce 50% or more of the high-FODMAP foods they’ve eliminated once their gut has calmed down 9. 

For help navigating this diet, download my Low FODMAP Diet Guide. 

Importantly, a low FODMAP diet not only helps relieve inflammation and pesky symptoms like indigestion and bloating, but it can also help pinpoint food intolerances you aren’t aware of. 

When it comes to food intolerance or food sensitivity, there’s more than lactose intolerance or celiac disease. You may have a sensitivity to a certain food category (like nightshades) or even just spicy foods. By removing and reintroducing, you can learn which foods your body can’t quite tolerate yet.

2. Elemental Diet: A Break Without Fasting

An elemental diet gives your gut all the nutrients it needs in pre-digested, liquid form. No fiber, no complex carbs, nothing for bacteria to ferment. It was developed as a medical food for severe gastrointestinal issues and medical conditions, usually used as the main source of calories for weeks. However, it can also be used in a short-term way to give you a “digestive vacation.” 

What happens during an elemental reset:

• Bacteria starve → gas production drops
• Immune activity calms down
• The gut lining gets a chance to heal

Studies from Dr. Mark Pimentel’s group show that 75–85% of SIBO patients who consumed an elemental diet exclusively for 2–3 weeks had normalized breath tests (an indication that SIBO is gone) 10 11. However, we’ve found that you can use it for a shorter window and see great results. 

Protocol

Here’s the elemental diet plan we use with our clients in the clinic:

• Full Gut Reset: 2–4 days of exclusive elemental diet
• Partial option: Use an elemental diet to replace 1–2 meals/day for 2–3 weeks

Our clinic developed Elemental Heal, the first over-the-counter elemental formula designed for easy use.

If you’re interested in a longer elemental diet reset, be sure to work with your healthcare provider.

3. Probiotics: Rebuild Tolerance, Not Just Flora

It’s no surprise that probiotics are often recommended for digestive issues—their reputation for supporting gut health is well-earned. Research consistently shows benefits across a range of concerns, from constipation to bacterial overgrowth.

For example, a meta-analysis found that probiotic supplements were helpful for bumping up stool frequency in people with constipation 12. Relieving constipation can help reduce the discomfort and pain that comes with it. 

Another meta-analysis found that probiotics alone resolved SIBO in over 50% of cases 13. Probiotics can also consistently reduce bloating and pain, and improve quality of life for IBS patients 14.

However, probiotics don’t just help the gut—certain probiotic strains may also support the immune system by 15:

• Boosting anti-inflammatory compounds like butyrate
• Reducing histamine-producing bacteria
• Increasing secretory IgA, your gut’s first line of defense

Protocol

In the clinic, I recommend that patients follow this plan for taking probiotics: 

• Begin taking them alongside diet changes.
• Use all three well-researched types: Lactobacillus/Bifidobacterium, Saccharomyces species, and soil-based (usually Bacillus) strains.
• Take 1–2 packets/day of Triple Therapy Probiotic for 4–8 weeks.

4. Botanicals + Enzymes: Clearing Overgrowth Strategically

Botanical antimicrobials can effectively reduce bacterial overgrowth. An added benefit is that they often do so with fewer side effects than antibiotics.

The top options we use in the clinic include:

• Berberine (for bacterial clearing + bile flow support)
• Oregano oil (a potent antifungal)
• Wormwood and black walnut (for broad-spectrum antimicrobial coverage)

A clinical trial found these herbs may outperform the antibiotic rifaximin at clearing SIBO 16.  

To make them more effective, we often pair them with biofilm-busting enzymes like protease and chitosanase to break down the walls encasing bacterial hiding spots. 

Protocol

Here’s the exact herbal antimicrobial protocol we use in the clinic:

• Month 1: Biota-Clear 1a/1b
• Month 2: Biota-Clear 2a/2b
• Add enzymes before meals for 4–6 weeks

We’re about to submit a paper documenting this protocol’s success—we’ll let you know when it’s published!

5. Vagus Nerve Stimulation: Rebooting the Gut-Brain Connection

The vagus nerve is sometimes referred to as your body’s superhighway, sending signals to and from your brain to the rest of your body. Stimulating this nerve with a vagus nerve reset can help improve its function, including digestion.

A particularly effective method is Auricular Vagus Nerve Stimulation (aVNS), which sends gentle electrical pulses through the ear to activate the vagus nerve and increase the release of acetylcholine. Acetylcholine is a neurotransmitter that helps regulate digestion, memory, and muscle contractions. 

By increasing the release of acetylcholine, aVNS can:

• Improve motility
• Reduce inflammatory cytokines
• Lower anxiety and pain sensitivity

In a 2024 randomized trial, just 30 minutes/day of aVNS increased levels of beneficial Bifidobacteria and improved both gut and mood symptoms in people with constipation-dominant IBS (IBS-C) 17. 

Protocol

In the clinic, we find the following is effective for stimulating the vagus nerve in our clients:

• Device: VaguStim or similar
• 15–30 minutes per session
• 1–2 sessions/day for 4–6 weeks

Vagus nerve stimulation isn’t just for symptom relief—it’s about rewiring the system.

Final Thoughts

If your stomach hurts after eating even healthy foods, the issue likely isn’t what you’re eating—it’s how your gut and nervous system are interpreting it.

By addressing potential bacterial overgrowth, calming any immune reactivity, and strengthening gut-brain communication, the five approaches outlined in this article can help restore tolerance—not just quiet the noise.

If you need help navigating your journey toward better digestive health, please reach out to us at the Ruscio Institute for Functional Health.

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.