I’ve lost count of how many clients come to me with a shopping bag full of supplements they’ve bought online, half-used bottles cluttering their kitchen bench, and genuine confusion about what they should actually be taking. The supplement aisle (or Instagram ads) promise quick fixes for leaky gut and food intolerances, but the reality is far more nuanced.
After 12 years of working with clients dealing with gut barrier issues and food reactivity, I’ve learned what actually moves the needle and what just empties your wallet. This isn’t about the latest trendy supplement or the “one weird trick” that influencers are pushing. It’s about practical, evidence-informed approaches that fit into real life.
Let me be clear upfront: supplements are tools, not magic bullets. They work best when they’re part of a broader strategy that includes diet, lifestyle, and addressing the root causes of your gut issues. But when used strategically, the right supplements can genuinely support your healing process.
Understanding What You’re Actually Dealing With
The Leaky Gut and Food Intolerance Connection
Before we dive into specific supplements, it helps to understand what’s actually happening in your gut. Intestinal permeability, often called leaky gut, occurs when the tight junctions between the cells lining your intestinal wall become compromised. Think of it like the grout between tiles becoming loose and allowing things to pass through that shouldn’t.
When this barrier becomes permeable, partially digested food particles, bacteria, and other compounds can pass into the bloodstream. Your immune system, doing its job, identifies these as foreign invaders and mounts an inflammatory response. This is often where food intolerances develop or worsen.
The tricky part? This creates a self-perpetuating cycle. The inflammation damages the gut barrier further, which allows more particles through, which triggers more inflammation. Breaking this cycle requires a multi-pronged approach, and that’s where targeted supplementation can help.
Why your triggers might be different from your friend’s: Everyone’s gut microbiome, inflammatory pathways, and immune responses are unique. The foods that set off your symptoms might be completely fine for someone else with similar issues. This is why cookie-cutter supplement protocols often disappoint.
Before You Buy Another Supplement
I always ask clients several questions before recommending anything:
- What have you already tried, and what was your response?
- What’s your current diet like, and are there obvious inflammatory triggers?
- How’s your stress level, sleep quality, and overall nervous system state?
- Are you dealing with other health conditions or taking medications?
- What’s your budget, and what can you realistically stick with?
These aren’t just nice-to-know details. They fundamentally shape what supplements will be most helpful and which ones might be a waste of money or even counterproductive.
Testing vs. trialling: Sometimes comprehensive stool testing or food intolerance panels make sense, especially if you’ve been struggling for a long time without clear answers. Other times, a strategic trial of key supplements alongside dietary changes is the more practical starting point. I help clients navigate this decision based on their individual situation and budget.
Key Point
If your current supplements aren’t working, it’s rarely because you need more supplements. Usually, it’s because the wrong ones were chosen, the dosing wasn’t right, or the underlying issues weren’t addressed. Quality and strategy matter far more than quantity.
The Core Supplements I Actually Use With Clients
L-Glutamine: The Gut Lining Workhorse
Glutamine is the primary fuel source for the cells lining your small intestine (enterocytes). When these cells are well-nourished, they can maintain those tight junctions we talked about earlier and repair damage more effectively.
In practice, I’ve seen glutamine make a real difference for clients, particularly those with gut barrier issues following gastro, prolonged stress, or inflammatory bowel conditions. It’s not flashy, but it’s foundational.
Dosing that works in real life: I typically start clients on 5-10 grams daily, often split into two doses. Some research uses higher doses (up to 30 grams daily), but I find the moderate range works well for most people without breaking the budget.
Timing matters: I usually recommend taking glutamine away from meals, either first thing in the morning and before bed, or mid-morning and mid-afternoon. This allows it to be preferentially used by the gut lining rather than being burned for general energy.
Powder vs. capsules: Powder is more cost-effective and easier to dose accurately, but some people prefer the convenience of capsules. If you go the capsule route, be prepared to take quite a few to reach therapeutic doses.
Who should be cautious: If you have kidney or liver issues, check with your doctor before using higher-dose glutamine. People with cancer should also discuss this with their oncologist, as glutamine can potentially feed rapidly dividing cells.
Zinc Carnosate: The Underrated Option
Zinc doesn’t get the same airtime as some trendier supplements, but it’s crucial for maintaining gut barrier integrity. It’s directly involved in the function of tight junction proteins and supports immune regulation in the gut lining.
Research shows that zinc deficiency is surprisingly common in people with chronic gut issues, partly because inflammation increases zinc requirements and partly because poor absorption is often part of the picture.
Practical dosing: I typically use 30-40mg of elemental zinc daily (as zinc carnosate, which is gentler on the stomach than some other forms). This is taken with food to minimise nausea, which some people experience with zinc on an empty stomach.
Duration matters: Unlike glutamine, which you might use longer-term, I usually run zinc supplementation for 2-3 months and then reassess. Long-term high-dose zinc can interfere with copper absorption, so it’s not something to take indefinitely without monitoring.
Signs you might need zinc support: Slow wound healing, frequent colds, white spots on nails, loss of taste or smell, and skin issues can all hint at low zinc status. But these are general signs, not definitive diagnosis.
Slippery Elm and Marshmallow Root: The Soothing Duo
These mucilaginous herbs create a protective coating along the digestive tract, which can be incredibly soothing when your gut lining is inflamed and reactive. Think of them as a protective barrier while your gut does its deeper healing work.
I reach for these particularly when clients describe a raw, burning sensation in their gut, or when they’re so reactive that even gentle foods trigger symptoms. The demulcent action provides symptomatic relief while other interventions address root causes.
Forms that work best: Powder is ideal because it mixes with water to create that mucilaginous gel, which is exactly what provides the benefit. Capsules work too, but you need to take them with plenty of water. Some clients love slippery elm as a warm, slightly sweet tea before bed.
The time-of-day factor: I often suggest taking these away from other supplements and medications because they can potentially interfere with absorption. First thing in the morning or last thing at night often works well, or mid-afternoon if you’re having reactive symptoms.
Combining with other protocols: These herbs work beautifully alongside other gut healing approaches without interfering. They’re gentle, safe long-term, and relatively inexpensive.
Quercetin: The Mast Cell Connection
Quercetin often comes up in discussions about food intolerances, particularly when histamine is part of the picture. It’s a plant compound (a flavonoid) that can help stabilise mast cells, which release histamine and other inflammatory mediators.
When your gut barrier is compromised, you often see increased mast cell activation. This can contribute to both the gut symptoms and the systemic reactions that many people experience with food intolerances.
Dosing strategies I use: Typically 500-1000mg daily, often split into two doses. Some protocols use higher amounts, but I find this range effective for most clients.
Who responds best: In my experience, people who describe reactions that seem out of proportion to what they’ve eaten, or who have symptoms beyond the gut (skin flushing, headaches, anxiety), often respond well to quercetin. It’s particularly relevant if you suspect histamine intolerance.
Realistic expectations: Quercetin isn’t a quick fix. Most clients notice benefits after 2-4 weeks of consistent use. It’s part of a bigger strategy, not a standalone solution.
Absorption tip: Quercetin is better absorbed when taken with vitamin C or bromelain (a pineapple enzyme). Some formulations include these co-factors.
Digestive Enzymes: Strategic Support
This is where I see a lot of confusion. Digestive enzymes can be genuinely helpful as a short to medium-term support, but they’re not meant to be a permanent crutch.
When enzyme support makes sense:
- When you’re eating foods that trigger symptoms but need to maintain some dietary variety while healing
- During the initial phases of addressing gut issues, to reduce the burden on your digestive system
- If you have confirmed insufficiency of specific enzymes (like lactase)
- As you’re reintroducing foods after an elimination diet
When it doesn’t make sense:
- As the sole intervention without addressing underlying issues
- Long-term without investigating why your natural enzyme production is inadequate
- If you’re already on a very restricted diet (you’re likely not challenging your digestion enough to need them)
The different types: Broad-spectrum enzymes include proteases (protein), lipases (fat), and amylases (carbohydrate). Some formulations add lactase for dairy, alpha-galactosidase for beans and cruciferous vegetables, or other specific enzymes. I choose based on what foods trigger the worst symptoms.
Weaning off as things improve: As your gut heals and inflammation reduces, you should find you need enzymes less frequently. I encourage clients to trial reducing them every few months to see if they’re still necessary. The goal is independence, not dependency.
Probiotics: The Complicated Player
If there’s one area where advice is all over the place, it’s probiotics. Everyone from your hairdresser to random internet gurus has an opinion on which probiotic you “must” take.
The research on probiotics for gut barrier function is genuinely promising, but it’s also incredibly strain-specific. What works for one condition may not work for another, and what helps one person might make another worse.
Strains that research supports for barrier function:
- Lactobacillus plantarum and L. rhamnosus have decent evidence for supporting tight junctions
- Saccharomyces boulardii (technically a beneficial yeast, not bacteria) can be helpful during and after gut infections
- Multi-strain formulations with a mix of lactobacilli and bifidobacteria often work well
The FODMAP and histamine considerations: This is crucial and often overlooked. If you’re sensitive to FODMAPs or dealing with histamine issues, some probiotics can actually worsen your symptoms. High-histamine strains include many lactobacilli, while Bifidobacterium strains are generally lower in histamine production.
Starting low and going slow: I’ve seen too many clients start a high-dose probiotic and feel significantly worse within days. Begin with a low dose (even half a capsule if needed) and increase gradually. If you feel worse, it doesn’t necessarily mean you “shouldn’t take probiotics.” It might mean you need a different strain or a slower approach.
When prebiotics fit in: Prebiotics feed beneficial bacteria, which sounds great in theory. In practice, if you have SIBO, severe dysbiosis, or are very reactive, prebiotics can cause significant bloating and discomfort. I usually address the gut lining and inflammation first, then consider adding prebiotics later in the process.
Key Point
There’s no single “best probiotic” for everyone. The right choice depends on your specific gut issues, sensitivities, and what you’re trying to achieve. If a probiotic makes you feel worse, trust that signal. Your gut is telling you something.
Supportive Players Worth Knowing About
Omega-3s and Anti-inflammatory Support
Chronic inflammation is both a cause and consequence of gut barrier issues and food intolerances. Omega-3 fatty acids (EPA and DHA) have well-established anti-inflammatory effects throughout the body, including the gut.
I don’t always prioritise omega-3s as a first-line gut supplement, but they’re valuable as part of a comprehensive approach, especially if there’s systemic inflammation involved.
Quality and dosing that matters: Look for products that specify EPA and DHA content (not just total fish oil). I typically suggest 2-3 grams of combined EPA/DHA daily for therapeutic effect. Triglyceride form is generally better absorbed than ethyl ester form.
EPA vs. DHA ratios: For inflammation, higher EPA relative to DHA is often preferable. Many products offer a 2:1 or 3:1 EPA:DHA ratio.
Vegan options: Algae-based omega-3s provide EPA and DHA without fish products. They’re more expensive but work just as well.
Vitamin A and D
Both of these fat-soluble vitamins play crucial roles in immune regulation and gut barrier maintenance. Deficiency in either can contribute to increased intestinal permeability.
The vitamin D conversation: Unless you’re getting regular sun exposure on a good portion of your body, you’re likely not making adequate vitamin D, especially if you live in southern Australia. But I don’t recommend loading up on vitamin D without testing first.
I usually suggest checking vitamin D levels and supplementing to reach optimal range (around 100-150 nmol/L), which for most people means 2000-4000 IU daily. Higher doses can be appropriate if you’re significantly deficient, but should be monitored.
Vitamin A considerations: True vitamin A (retinol) comes from animal sources. Beta-carotene from plants needs to be converted to active vitamin A, and this conversion is inefficient in many people, particularly if you have gut issues. Cod liver oil provides both vitamin A and D, plus omega-3s.
Co-factor considerations: Vitamin D works synergistically with magnesium, vitamin K2, and vitamin A. If you’re supplementing vitamin D long-term, consider whether you’re getting adequate amounts of these co-factors.
Aloe Vera Inner Leaf
Aloe vera has been used for digestive issues for centuries, and there’s some good research supporting its use for gut inflammation and barrier function. The key is using the right part of the plant.
Inner leaf vs. whole leaf: You want inner leaf aloe, which is the gel-like substance from inside the leaf. Whole leaf preparations include the outer rind, which contains compounds with strong laxative effects (aloin and emodin). These can be irritating and aren’t what we’re after for gut healing.
When it’s helpful: I find aloe particularly useful for clients with inflammatory bowel conditions or persistent gut inflammation. It has soothing, anti-inflammatory, and potentially prebiotic properties.
Quality matters more than you’d think: The aloe supplement industry is plagued by quality issues. Look for products that specify they’re from inner leaf, are preservative-free, and ideally certified by the International Aloe Science Council (IASC).
How I use it in protocols: Usually 50-200ml of aloe juice daily, taken away from meals. Some people prefer it chilled or mixed with a small amount of juice. Start with a smaller amount to ensure you tolerate it well.
What You Won’t Find Here (And Why That’s Okay)
The Overhyped Stuff
I’m not going to recommend every supplement that has “gut health” in its marketing copy. Some products have impressive advertising budgets but underwhelming evidence. Others might work for specific situations but aren’t the universal solutions they’re sold as.
Bone broth protein powders: Real bone broth can be nourishing and provides glutamine and glycine. Expensive powdered versions? Often just glorified protein powder without the benefits of actual broth. If you want the benefits of bone broth, make actual broth.
Collagen supplements for gut healing: While collagen provides amino acids including glycine and proline, the evidence for it specifically healing leaky gut is thin. It’s not harmful, but it’s also not essential if you’re already using other approaches.
Expensive proprietary blends: Some supplement companies create fancy formulations with a dozen ingredients and charge premium prices. Often, you’d get better results with a few targeted, high-quality individual supplements.
Reading through supplement claims with a critical eye: If a supplement promises to “heal leaky gut in 30 days” or “eliminate all food sensitivities,” be sceptical. Gut healing is a process, not an event. Quality companies make evidence-based claims, not miracle promises.
The “Everyone Should Take This” Myth
I don’t believe in one-size-fits-all supplement protocols. Your gut issues developed in a specific context (your genetics, history, stressors, diet, microbiome), and they’ll respond best to an individualised approach.
Budget realities and prioritising: Most people can’t afford to take everything that might be helpful. That’s fine. I’d rather see someone take 2-3 well-chosen supplements consistently than buy a dozen bottles that sit in the cupboard because it’s too overwhelming.
If budget is tight, I usually prioritise:
- L-glutamine for gut lining support
- A quality probiotic (chosen for your specific situation)
- Zinc if there are signs of deficiency
Everything else can be added as budget allows and as we see what’s working.
Building a Practical Protocol That Fits Your Life
The Staged Approach I Use
I don’t throw everything at the problem at once. Starting too many supplements simultaneously makes it impossible to know what’s helping, what’s not, and what might be causing new symptoms.
Phase 1 (Weeks 1-4): Start with gut lining support
- L-glutamine
- Slippery elm or marshmallow root if there’s significant inflammation
- Basic dietary modifications to remove obvious triggers
Phase 2 (Weeks 4-8): Add targeted support based on response
- Zinc if barrier function still seems compromised
- Quercetin if histamine/mast cell issues are evident
- Digestive enzymes if needed for symptom management
Phase 3 (Weeks 8-12): Fine-tune and add supportive nutrients
- Probiotics (introduced carefully)
- Omega-3s if systemic inflammation is present
- Any other targeted support based on individual needs
How long to trial before assessing: Give each addition at least 2-4 weeks before deciding if it’s helping. Some supplements work quickly, others need time. Keep notes on symptoms, energy, digestive function, and any changes you notice.
Supplement Timing and Combinations
Getting timing right can make a surprising difference to how well supplements work and how easy they are to stick with.
What to take when:
- First thing in morning (empty stomach): L-glutamine, slippery elm
- With breakfast: Probiotics, omega-3s, zinc, vitamin D
- With lunch: Digestive enzymes (if using), quercetin
- With dinner: Digestive enzymes, quercetin, omega-3s
- Before bed (empty stomach): L-glutamine, marshmallow root
Simplifying so you’ll actually stick with it: If the above s
