The Hidden Connection Between Celiac, Leaky Gut, and Autoimmunity

For many people diagnosed with celiac disease, the path forward seems clear: eliminate gluten, and symptoms will improve. But what happens when you do everything “right”- follow a strict gluten-free diet, read every label, and avoid cross-contamination - and you still feel bloated, fatigued, foggy, or inflamed?

This is an increasingly common experience, and it points to a deeper issue that often goes unaddressed: leaky gut.

Celiac isn’t just a food intolerance – it’s an autoimmune response that damages the gut lining. That damage doesn’t always stop with gluten removal. In fact, for many people, the immune system remains activated, the gut stays permeable, and other health concerns begin to emerge - especially autoimmune conditions.

Emerging research shows that intestinal permeability (commonly known as leaky gut) is not just a symptom of celiac disease - it may be a key driver of the systemic inflammation and autoimmunity that can follow. The gut barrier is meant to be a gatekeeper. When it’s compromised, everything changes.

In this blog, we’ll explore the powerful connection between celiac disease and leaky gut - and how that relationship can set the stage for broader autoimmune dysfunction. More importantly, we’ll walk through what can be done to repair the gut, regulate the immune system, and restore your health beyond gluten-free eating alone.

Whether you’re newly diagnosed or years into your celiac journey and still not feeling well, this post will help you understand what’s really going on and how to begin healing from the inside out.

What is Celiac Disease? A Quick Refresher

Celiac disease is more than just a gluten intolerance; it’s an autoimmune condition that causes the body to attack its own intestinal lining in response to gluten, a protein found in wheat, barley, and rye. When someone with celiac disease eats gluten, their immune system mistakenly identifies it as a threat and launches an inflammatory response that damages the small intestine.

This immune reaction primarily targets the villi, small, finger-like projections that line the small intestine and are responsible for absorbing nutrients. Over time, repeated exposure to gluten flattens and damages the villi, leading to malabsorption of key nutrients like iron, B12, calcium, zinc, and fat-soluble vitamins.  

Common symptoms of celiac disease include:

• Bloating and abdominal discomfort

• Chronic diarrhea or constipation

• Nutrient deficiencies (often iron or B vitamins)

• Fatigue or low energy

• Brain fog and difficulty concentrating

• Skin rashes (e.g., dermatitis herpetiformis)

• Unexplained weight loss or difficulty gaining weight

• Infertility or menstrual irregularities

• Mood changes or anxiety

It’s important to note that not everyone with celiac disease experiences digestive symptoms. Some people may have silent or non-classical celiac disease, where symptoms are extra-intestinal, such as fatigue, joint pain, or neurological symptoms, and may go unrecognized for years.

Celiac disease is different from gluten sensitivity

Unlike non-celiac gluten sensitivity (which may trigger discomfort but doesn’t involve immune-mediated intestinal damage), celiac disease is an autoimmune condition with long-term consequences. Left unmanaged, it can increase the risk of:

• Osteoporosis

• Infertility

• Neurological conditions

• Liver disease

• Other autoimmune disorders (such as Hashimoto’s thyroiditis or type 1 diabetes)

The cornerstone of celiac treatment is a strict, lifelong gluten-free diet. Even tiny amounts of gluten can cause inflammation and damage.

But what many people don’t realize is that for some, removing gluten doesn’t resolve all symptoms. In fact, many people with celiac disease continue to experience fatigue, bloating, food sensitivities, or skin issues even after going gluten-free. This is often due to a related—but less often discussed—issue: leaky gut.

In the next section, we’ll explore exactly how gluten contributes to intestinal permeability in people with celiac disease—and why this matters for long-term health and immune regulation.

How Gluten Triggers Leaky Gut in Celiac Disease

The lining of your small intestine isn’t just a passive surface for digestion; it’s a highly selective barrier. Its role is to allow nutrients into your bloodstream while keeping harmful substances, pathogens, and undigested food particles out. This protective barrier is made up of tightly packed cells connected by structures called tight junctions.

In a healthy gut, these tight junctions open and close as needed. But in celiac disease, this regulation breaks down, and gluten plays a central role in this disruption.

Gluten, zonulin, and the gut barrier

When someone with celiac disease consumes gluten, it triggers the release of a protein called zonulin. Zonulin acts like a gatekeeper for the tight junctions between cells in the intestinal lining. In small, temporary amounts, zonulin plays a useful role. But in celiac disease, gluten exposure causes zonulin levels to spike abnormally, prying open the gut barrier.

This leads to intestinal permeability – also known as leaky gut – where substances that are normally kept inside the digestive tract are now allowed to pass into the bloodstream.  

These substances may include:

• Undigested food proteins

• Pathogenic microbes or their by-products (like LPS)

• Toxins

• Inflammatory compounds

Once in the bloodstream, these particles are flagged as foreign invaders by the immune system, which launches a defensive response. This adds to the inflammatory burden and contributes to a cycle of gut damage, immune activation, and further barrier breakdown.

Why leaky gut doesn’t always resolve with a gluten-free diet

A gluten-free diet is essential for managing celiac disease – but in many people, leaky gut persists even after strict dietary changes. That’s because the factors contributing to intestinal permeability aren’t limited to gluten alone.

• Persistent leaky gut can be driven by:

• Ongoing immune system activation

• Dysbiosis (imbalanced gut microbiota)

• Inflammation that has yet to resolve

• Nutrient deficiencies (e.g., zinc, vitamin D, glutamine

• Stress, which directly affects gut barrier function via the gut-brain axis

This is why some people continue to experience bloating, fatigue, food sensitivities, and inflammatory symptoms even while strictly avoiding gluten.

Why this matters

Leaky gut is more than just a gut issue – it’s an immune system issue. When the gut barrier breaks down, the immune system becomes overactive and confused. Over time, this can lead to systemic inflammation and increase the risk of developing additional autoimmune diseases – a phenomenon that is well-documented in people with celiac disease.

In the next section, we’ll explore how leaky gut contributes to the development of autoimmune conditions – and why healing the gut lining is essential for both symptom relief and long-term immune resilience.

Leaky Gut and Autoimmunity: The Domino Effect

Autoimmune disease doesn’t just happen overnight. It’s the result of a complex interplay between genetics, environment, immune triggers, and increasingly, gut health. For those with celiac disease, the gut is not the only primary site of damage, but also the launch point for broader immune dysfunction.  

One of the key mechanisms behind this progression is leaky gut, or intestinal permeability.

How a compromised gut barrier fuels autoimmune disease

When the gut lining becomes permeable, it allows substances to cross into the bloodstream that were never meant to leave the digestive tract, including:

• Undigested food particles

• Lipopolysaccharides (LPS), an inflammatory component of bacterial cell walls

• Toxins or environmental chemicals

• Microbial fragments

Once these particles enter the bloodstream, the immune system identifies them as threats and responds accordingly. But here’s where things can go wrong: some of these particles resemble tissues in your own body.

This is known as molecular mimicry.

Why people with celiac disease are at a higher risk for autoimmunity

Celiac disease is already an autoimmune condition. But due to the combination of chronic inflammation, gut permeability, and immune system hyperactivation, people with celiac disease are at significantly higher risk for developing additional autoimmune diseases.

Some of the most commonly associated conditions include:

• Hashimoto’s thyroiditis (autoimmune hypothyroidism)

• Type 1 diabetes

• Rheumatoid arthritis

• Psoriasis

• Sjogren’s syndrome

• Autoimmune liver disease

• Multiple sclerosis (in some cases)

According to research, up to 30% of people with celiac disease will develop at least one other autoimmunity disorder – a risk that may be increased when leaky gut remains unresolved.

Gut health and immune regulation

The integrity of the gut lining plays a crucial role in modulating immune tolerance – the ability of the immune system to differentiate between what belongs and what doesn’t.

When the gut is intact, it acts as a filter and a teacher: educating the immune system, containing inflammatory triggers, and maintaining balance. But when that barrier is compromised, the immune system becomes more reactive, less selective, and increasingly prone to misfire.

This is why gut repair is about more than relieving digestive symptoms; it’s about calming immune confusion and preventing further autoimmune damage.

In the next section, we’ll look at why simply removing gluten often isn’t enough to fully heal the gut, and what else needs to be addressed to truly restore function and immune balance.

Why Going Gluten-Free Isn’t Always Enough

For those diagnosed with celiac disease, removing gluten is non-negotiable. A strict gluten-free diet is essential to stop the autoimmune attack, prevent further intestinal damage, and reduce long-term complications.

But many people discover that even after months (or years) of avoiding gluten, they still don’t feel well.

If that’s your experience, you’re not alone, and you’re not imagining it. The truth is, while going gluten-free is the first step, it’s often not the last step in the healing process.

Gluten removal stops the trigger, not the damage

Think of gluten as the spark, but leaky gut and chronic inflammation as the fire that continues to smoulder long after the spark is gone.

When gluten is removed, the immune system may calm down – but the gut lining still needs to rebuild itself. This process depends on more than just time. It requires nutrient support, microbiome rebalancing, stress regulation, and sometimes addressing coexisting imbalances that gluten-free living alone won’t resolve.

Common reasons symptoms persist on a gluten-free diet:

Persistent leaky gut

• The gut lining may still be compromised due to previous damage or ongoing inflammation

• Without active repair, permeability can remain high – keeping the immune system on alert.

Dysbiosis (microbial imbalance)

• Celiac-related gut damage often affects microbial diversity.

• A gluten-free diet doesn’t necessarily restore the microbiome, especially if low in plant fibre.

Nutrient deficiencies

• Malabsorption during active celiac often leads to deficiencies in zinc, B12, folate, iron, magnesium, vitamin D, and L-glutamine – all critical for gut repair.

• These deficiencies may persist if not specifically addressed.

Secondary food sensitivities

• Leaky gut can trigger immune reactions to other foods (e.g., dairy, eggs, soy), leading to lingering symptoms.

• These sensitivities may resolve once the gut heals – but can cause confusion in the meantime.

Ongoing inflammation or stress

• Emotional stress, poor sleep, overtraining, and environmental toxins can all perpetuate gut inflammation.

• The gut-brain connection means stress can directly impair digestion and immune regulation.

Coexisting gut issues

• SIBO (small intestinal bacterial overgrowth), candida overgrowth, or parasites may be present – and undiagnosed.

• These conditions often develop in the aftermath of celiac-induced gut disruption.

A gluten-free diet is necessary, but not sufficient

Think of it this way: going gluten-free removes the source of damage, but it doesn’t rebuild what’s already been damaged. That’s where a functional approach comes in – one that focuses on repairing the gut lining, restoring microbial balance, calming inflammation, and regulating the immune system.

In the next section, we’ll walk through a step-by-step gut-healing framework designed specifically for post-celiac recovery – so you can move beyond symptom management and toward true, lasting health.

Healing the Gut Lining After Celiac Damage

Removing gluten is critical, but it’s not enough to fully repair the gut lining or calm the immune system. True healing after celiac disease requires a multiphase approach that addresses the integrity of the gut barrier, microbial balance, inflammation, and immune modulation.

Here’s how to move from damage control to gut restoration.

Phase 1: Remove what’s aggravating the gut

This goes beyond gluten. In the early stages of healing, it’s important to reduce or temporarily eliminate other common triggers that may keep the gut inflamed.

This might include:

• Cross-reactive foods like dairy, soy, or corn (temporarily)

• Ultra-processed, low-nutrient foods that provide little repair support

• Environmental toxins (minimize exposure to pesticides, plastics, heavy metals)

• Stress and poor sleep, which directly affect gut lining repair and immune activation

• Chronic infections, SIBO, or candida overgrowth (consider stool testing if symptoms persist)

This phase is not about long-term restriction—it’s about removing obstacles to healing, not eliminating foods forever.

Phase 2: Repair the gut lining

Once triggers are reduced, the next step is to rebuild the structural and functional integrity of the intestinal barrier.

Key nutrients and compounds to support this phase:

• L-glutamine: The preferred fuel for intestinal cells; supports regeneration

• Zinc carnosine: Clinically shown to support mucosal healing and reduce inflammation

• Collagen peptides: Provide key amino acids (glycine, proline) for tissue repair

• Slippery elm, marshmallow root, aloe vera: Mucilaginous herbs that soothe irritation and protect the lining

• Tegricel colostrum: Contains immunoglobulins and growth factors to aid repair

This is often the phase where symptoms like bloating, food reactions, and fatigue begin to improve—as the gut lining becomes more resilient.

Phase 3: Rebalance the Microbiome

Celiac-related gut damage is often accompanied by dysbiosis—and imbalance of good and opportunistic bacteria. Restoring microbial balance is essential for long-term gut and immune health.

Support this strain with:

• Strain-specific probiotics (e.g., Lactobacillus plantarum, Bifidobacterium breve)

• Prebiotic fibre from a variety of plant foods. Aim for 20-30+ different plant types/week

• Short-chain fatty acids (SCFA) production, which nourishes colon cells and reduces inflammation

• Fermented foods (if tolerated) like sauerkraut, kefir, or kimchi

Functional stool testing (like the GI-Map) can help identify overgrowths, deficiencies, or infections that need targeted support.

Phase 4: Regulate the immune response

Leaky gut and chronic inflammation can leave the immune system hypervigilant. Once the gut is on the path to healing, it’s essential to support immune tolerance and reduce reactivity.

Key strategies include:

• Stress regulation: Breathwork, vagus nerve stimulation, nervous system calming

• Sleep optimization: A cornerstone for immune and gut repair

• Vitamin D: Critical for immune modulation and tight junction integrity

• Omega-3 fatty acids: Anti-inflammatory and supportive of cell membrane repair

• Curcumin and quercetin: Anti-inflammatory compounds that help stabilize mast cells and reduce reactivity

This phase often marks the transition from symptom management to resilience – where the gut and immune system can handle more flexibility, more foods, and fewer flare-ups.

Healing the gut lining after celiac damage isn’t about perfect, it’s about providing your body with what it needs to repair. When this process is done strategically and patiently, it’s possible to rebuild tolerance, restore energy, and prevent progression of autoimmune issues.

In the final section, we’ll recap the key takeaways – and how working with a practitioner can help guide this process step by step.

Final Thoughts: From Gluten-Free to Gut Healing

Celiac disease doesn’t end with gluten. For many people, it’s the start of a deeper journey – one that involves rebuilding the gut, calming the immune system, and preventing further autoimmune damage.

If you’ve been gluten-free but still feel unwell, that doesn’t mean you’re doing anything wrong. It means your gut may still be healing. Leaky gut, nutrient depletion, microbial imbalance, and lingering inflammation are all common after celiac—and they’re all addressable with the right support.

Understanding how gluten affects the gut barrier – and how that contributes to immune dysfunction – is a critical step toward lasting wellness. And while going gluten-free removes the trigger, a full recovery often requires a more holistic, functional approach.  

If this resonates with you…

You don’t have to keep guessing what’s going on with your gut. Testing like the GI-Map can uncover what’s really happening beneath the surface – and a tailored plan can help restore balance, step by step.

If you’re ready to move from surviving on a gluten-free diet to actually thriving, I invite you to book a free discovery call. We’ll explore what’s still holding you back and how gut repair could be the missing piece in your healing.

You deserve to feel well again – not just glute-free, but truly supported from the inside out.