Why You’re Still Bloated, Even After Cutting Out Gluten

A naturopathic deep dive into gut imbalances, hidden triggers, and lasting relief

You’ve done all the right things. You cut out gluten. You tried going dairy-free. You’ve sipped your peppermint tea, taken the probiotics, and even passed on dessert more times than you can count.

And yet… you’re still bloated.

Every afternoon, your belly swells like a balloon. Your pants feel tighter by dinner. You might look a few months pregnant by the end of the day. Sound familiar?

If so, you’re not alone—and you’re not imagining it.

At Prairie Naturopathic Doctors, we hear this story every day in our clinics. Many of our patients come to us feeling confused, frustrated, and discouraged. They’ve done what conventional advice told them to do—cutting out gluten, eating “clean,” taking over-the-counter remedies—but still feel weighed down by digestive discomfort.

Here’s what we want you to know: bloating is not just about what you eat. It’s also about how your gut is functioning—and that’s where Holistic Health, Naturopathic Medicine, and individualized care come in.

Let’s take a closer look at why bloating lingers even after eliminating gluten—and what you can do to finally get lasting relief.

 

First, Why Does Gluten Get the Blame?

Gluten—a protein found in wheat, barley, and rye—can be a digestive irritant for some people. For those with celiac disease, gluten damages the small intestine and must be strictly avoided. Others may have non-celiac gluten sensitivity, which can cause gas, bloating, fatigue, and brain fog.

But here’s the problem: going gluten-free is often treated as a one-size-fits-all solution for bloating. And while some people do improve with gluten elimination, many don’t. Or their symptoms return later—despite maintaining a strict gluten-free lifestyle.

So if gluten isn’t the root cause for everyone, what is?

 

5 Hidden Reasons You Might Still Be Bloated

Let’s explore the most common reasons we see patients still struggling with bloating—even after making big dietary changes. And more importantly, how we approach them using Natural Remedies, Herbal medicine and Supplements, Nutritional Therapy, and Nutritional Therapy and Physiotherapy.

 

1. Gut Dysbiosis: When Microbes Get Out of Balance

Your digestive system is home to trillions of bacteria, fungi, and viruses—collectively known as your gut microbiome. These microbes play a major role in digestion, immunity, metabolism, and even mental health.

But when the balance is disrupted—a state called dysbiosis—it can lead to digestive chaos.

Symptoms of Gut Dysbiosis:

• Chronic bloating and gas
   
• Constipation or loose stools
   
• Unexplained food sensitivities
   
• Brain fog or fatigue
   
• Bad breath
   
• Skin issues like acne, eczema, or rosacea
   
• Sugar cravings
   

Dysbiosis can be triggered by:

• Antibiotic use (even years ago)
   
• Diets high in sugar or processed food
   
• Chronic stress
   
• Long-term use of antacids or NSAIDs
   
• Infections like food poisoning
   

Even people who eat a clean, organic, gluten-free diet can still have dysbiosis if the terrain of the gut has been compromised.

How We Treat It:

At Prairie Naturopathic Doctors, we use testing and functional analysis to assess your microbiome. We then support you with targeted gut flora balancing herbal medicines, microbiome rebuilding, gut-lining support, and diet strategies based on Nutritional Therapy.

 

2. Enzyme Deficiencies: You Can’t Absorb What You Don’t Break Down

Enzymes are the unsung heroes of digestion. These proteins break down your food into smaller pieces so your body can absorb nutrients.

Without enough enzymes, food sits in your gut too long. It ferments, feeds gas-producing bacteria, and causes—you guessed it—bloating.

Signs of Enzyme Deficiency:

• Bloating within 30 to 60 minutes of eating
   
• Fullness that lingers for hours
   
• Gas and burping after meals
   
• Floating or greasy stools
   
• Undigested food in stool
   
• Fatigue after eating
   
• Nausea with high-fat foods
   

Enzyme issues can come from:

• Low stomach acid (often misdiagnosed as acid reflux)
   
• Aging
   
• Chronic stress
   
• Gallbladder issues or gallbladder removal
   
• Pancreatic insufficiency
   
• Inflammatory gut conditions
   

Even healthy eaters can struggle with this. Raw vegetables, beans, nuts, and lean meats can be difficult to break down without the right enzyme activity.

How We Treat It:

We prescribe digestive enzyme supplements tailored to your specific deficiencies. For example, lipase helps with fats, protease with proteins, and amylase with carbs. We rehabilitate the digestive organs and support stomach acid production, bile flow, and pancreatic health through Naturopathic Physiotherapy.  We also support digestive function with Herbal medicine and Supplements and Nutritional Therapy.

 

3. SIBO (Small Intestinal Bacterial Overgrowth): Bacteria in the Wrong Place

SIBO occurs when bacteria that belong in your large intestine migrate up into your small intestine—where they shouldn’t be. Once there, they ferment the food you eat and produce gas as a byproduct.

This gas becomes trapped in the small intestine, which leads to significant bloating, pressure, and discomfort.

Common SIBO Symptoms:

• Bloating that gets worse as the day goes on
   
• Gas that smells sulfuric or foul
   
• Belching after meals
   
• Nausea
   
• Constipation, diarrhea, or alternating between both
   
• Brain fog
   
• Nutrient deficiencies (especially iron and B12)
   
• Weight changes (gain or loss)
   

SIBO often masquerades as IBS. In fact, studies suggest that over 70% of IBS cases are actually SIBO.

SIBO can result from:

• Food poisoning
   
• Abdominal surgery
   
• Chronic stress
   
• Low stomach acid
   
• Sluggish motility or constipation
   
• Hormonal changes or thyroid disorders
   

How We Treat It:

We use SIBO breath testing to assess gas levels (hydrogen, methane, or hydrogen sulfide). Treatment is multi-phased:

1. Reduce bacterial overgrowth using Natural Remedies and herbal antimicrobials
    
2. Repair gut lining with nutrients like glutamine, zinc, and aloe
    
3. Restore motility with herbs like ginger or 5-HTP
    
4. Reintroduce a nourishing, anti-inflammatory diet—not forever-restrictive plans
    

Many patients see a dramatic reduction in bloating within the first few weeks of starting a tailored plan.

 

4. Nervous System Dysregulation: The Gut-Brain Connection

Your gut isn’t just a digestion machine. It’s deeply connected to your nervous system through the vagus nerve, a two-way highway between your brain and digestive organs.

If your nervous system is constantly stuck in fight-or-flight mode, your digestion will shut down. That means:

• Less enzyme production
   
• Poor bile flow
   
• Sluggish motility
   
• Increased sensitivity to gas or pressure
   

And yes—this all leads to bloating.

Symptoms of Nervous System Imbalance:

• Tension in your belly without obvious food triggers
   
• Anxiety or panic with digestive symptoms
   
• Bloated even on an empty stomach
   
• Shallow breathing or jaw clenching
   
• Sleep disturbances
   
• Feeling “stuck” in your body
   

This is why bloating often appears in highly sensitive, high-achieving people. Their systems are overloaded—and the gut is the first place it shows.

How We Treat It:

This is where Holistic Health shines. We may incorporate:

• Vagus nerve activation (cold exposure, singing, humming, gargling)
   
• Somatic practices to reconnect with your body
   
• Breathwork and restorative movement

 

• Visceral Manipulation to the fascia surrounding the abdominal organs
   
• Adaptogenic herbs like ashwagandha or gotu kola
   
• Nervine botanicals like skullcap, lemon balm, or passionflower

 

When the nervous system calms down, the gut often follows.

 

5. Hormonal Imbalances: Estrogen, Cortisol, and Thyroid Connections

Your hormones influence digestion far more than most people realize. Women often experience bloating tied to their menstrual cycles—and it’s not always due to food.

Hormone-Related Bloating Can Come From:

• Estrogen dominance (too much estrogen relative to progesterone)
   
• Low thyroid function (slows metabolism and gut motility)
   
• Elevated cortisol from chronic stress
   
• PCOS and insulin resistance
   
• Perimenopause or menopause
   

Hormonal bloating often includes:

• Puffiness around the midsection
   
• Water retention
   
• Constipation around ovulation or menstruation
   
• Breast tenderness, mood swings, or cravings
   
• Bloating that fluctuates with your cycle
   

How We Treat It:

We use hormone testing and symptom mapping to determine the source. Support may include:

• Liver detox support (since estrogen is processed in the liver)
   
• Herbal hormone balancers like chaste tree, maca, or dong quai
   
• Thyroid nutrients like selenium, iodine, and tyrosine
   
• Blood sugar balancing through Nutritional Therapy
   
• Stress reduction to normalize cortisol
   

Bloating from hormones often responds quickly when the whole system is supported—not just digestion alone.

 

Final Thoughts: You Don’t Have to Live With Bloating

If you’re still bloated after cutting out gluten, you’re not broken—and you’re not alone.

We specialize in helping people uncover the real reasons behind their symptoms using Naturopathic Medicine, Natural Remedies, Naturopathic Physiotherapy, Herbal medicine and Supplements, and advanced Nutritional Therapy.

We don’t just hand you a probiotic and wish you luck. We listen. We test. We customize. And we walk with you every step of the way until your belly feels calm, light, and functional again.