Understanding Food Sensitivities: A Root-Cause Approach to Gut Health, Elimination Diets, and Getting Back to Food
By Kendra Bova, MS, RDN, CDN, IFNCP — Functional Registered Dietitian Nutritionistinterviewed on the Fed by Science podcast by Claire Goldwitz, founder of Square Fare
The Zesty Piccata Bowl with Chicken Piccata Meatball, Roasted Potatoes, Spinach, Broccoli, Green Beans, Garlic, Parsley, Lemon Zest, Lemon Caper Sauce from Square’s Fare Menu, inspired by a recipe from Kendra Bova, MS, RDN
Overview
If you've recently received a food allergy panel showing a long list of reactive foods, you're likely wondering how seriously to take it and whether eliminating all of those foods is really necessary. The short answer is: not always. Food sensitivity testing is one of the most misused tools in nutrition, and a positive result does not automatically mean a food needs to be permanently removed from your diet.
Many people arrive at my practice holding a long list of foods they've been told to avoid, significant anxiety around eating, and no clear path forward. In this post, I want to clarify the differences between these conditions, explain why food allergy testing is often an unreliable starting point, and walk through the elimination diet process I use as the most evidence-based tool for identifying true triggers. I also share five practical tips for managing food restrictions in daily life without compromising nutrition or quality of life, including how the right meal support can make the difference between following through on a protocol and abandoning it entirely.
"Your labs are fine", — but you know something's wrong
One of the most common patterns I see is a patient who has visited multiple providers, had standard bloodwork done, and been told everything looks normal, despite continuing to experience real, persistent symptoms: bloating, fatigue, skin flares, poor sleep, brain fog.
Standard lab reference ranges are built around broad population averages. Being within range means you're not in the most concerning category, but it doesn't mean you're functioning optimally. In my practice, I look at patterns over time, connect symptoms that conventional medicine often evaluates in isolation, and ask not just "are you sick?" but "are you feeling your best?"
Gut health is a clear example of where this matters. Skin concerns, fatigue, and hormonal symptoms all have documented connections to gut function, and yet they're rarely evaluated together in a standard clinical workup. The Institute for Functional Medicine recognizes this root-cause, whole-systems approach as the foundation of functional nutrition practice.
Food allergies, sensitivities, and intolerances: understanding the distinctions
These three terms are frequently used interchangeably, but they describe different physiological processes, and should be assessed and treated differently.
A food allergy is an IgE-mediated immune response. Reactions are typically immediate, measurable through standard testing, and can range from mild symptoms to anaphylaxis. According toFood Allergy Research & Education (FARE), true food allergies affect approximately 6% of children and 4% of adults in the United States.
A food sensitivity or intolerance involves a delayed, non-IgE-mediated reaction, often appearing hours or a full day after consuming the trigger food. Bloating, fatigue, skin irritation, and brain fog are common presentations. Because the reaction is delayed and diffuse, many people live with food sensitivities for years without connecting their symptoms to specific foods.
For clinical purposes, I treat sensitivities and intolerances similarly in the early stages. Regardless of the underlying mechanism, the approach involves identifying the trigger, removing it, supporting gut healing, and determining whether long-term avoidance is necessary or whether reintroduction is possible once the gut has recovered.
Why I don't lead with food allergy testing
If my panel shows a reaction to a food, does that mean I can never eat it again?
Not necessarily, and this is one of the most important things I want patients to understand. A positive result on a food sensitivity panel indicates that your immune system has produced antibodies in response to a food protein, but it doesn't tell you whether that reaction is clinically significant, how severe your actual symptoms would be, or whether the sensitivity is permanent.
Food sensitivities are frequently a downstream effect of gut inflammation, not a fixed characteristic of your immune system. When the gut lining is compromised (a state sometimes called increased intestinal permeability) the immune system encounters food particles it wouldn't normally be exposed to and produces a response. Heal the gut, and that reactivity often resolves. I see this regularly in practice: patients who tested reactive to a food tolerate it without issue after a period of gut healing and structured reintroduction.
This is why I use allergy testing as context, not as a prescription. A panel that says you're reactive to eggs, almonds, and gluten is a starting point for investigation, not a permanent diagnosis.
Many patients arrive having already completed a food allergy panel, or requesting one as a first step. My approach tends to surprise them: I rarely order food allergy testing at the outset, and I'm cautious about how I use results when they exist.
The most commonly marketed panels, including IgG food sensitivity tests, have significant limitations.Published research has documented false positive rates and raised questions about clinical relevance. A food appearing positive on a panel doesn't necessarily mean the body is reacting to it in a meaningful way. Following these results too literally leads to extreme restriction that is often both unnecessary and counterproductive.
The more significant clinical concern is what I observe consistently: patients who arrive having eliminated 20 or 30 foods based on allergy testing, who are nutritionally depleted, anxious around food, and no closer to understanding what's actually driving their symptoms. Food fear, or the anxiety and hypervigilance that develops around eating, becomes its own problem, and addressing it becomes as much a part of the work as identifying true triggers.
Starting with the gut: why stool testing comes first
Rather than beginning with food elimination, my first step for most patients with suspected sensitivities is a comprehensive stool test. Most food sensitivities don't occur in isolation. They develop and persist in the context of gut inflammation, disrupted microbiome composition, or compromised intestinal barrier function. Addressing those underlying conditions changes the entire picture.
One marker I pay close attention to is eosinophil protein X (EPX), an inflammatory protein measurable in stool. When EPX is elevated, it signals active immune activation in the gut lining and serves as an early indicator that food-related immune responses may be contributing to symptoms. Research published inClinical and Experimental Allergy has examined EPX as a marker of gastrointestinal inflammation in the context of food sensitivity.
This distinction matters clinically because it reframes the goal. If the gut environment is inflamed and compromised, removing a type of food can address a symptom instead of a cause. TheAmerican Gastroenterological Association has documented the relationship between intestinal permeability and heightened immune reactivity to food antigens, supporting the importance of treating the gut environment itself, not just the food exposure.
The hopeful implication: food sensitivities are often not permanent. When gut inflammation resolves and the intestinal barrier repairs, foods that previously triggered reactions frequently become tolerable again. This is something I see consistently in practice, and it's important for patients to understand before they assume a sensitivity defines their diet indefinitely.
The elimination diet: the gold standard for identifying triggers
The elimination diet remains the most reliable clinical tool I have for identifying food sensitivities. The process follows three defined phases.
Phase 1: Elimination
The most common trigger foods are removed simultaneously for a defined period, typically three to four weeks. Standard protocols target gluten, dairy, soy, eggs, corn, and caffeine. I also flag less obvious triggers that patients often don't anticipate: nightshades (particularly relevant in cases ofSIBO or IBS), almond flour, protein powders, and collagen supplements. Foods that carry a wellness reputation are not exempt from being personal triggers.
The goal of Phase 1 is to reduce total inflammatory load and bring the gut to a quieter baseline where the body's signals become clearer.
This is where the practical challenge begins. The elimination phase requires significant dietary modification, often all at once. Implementation, or actually eating in alignment with the protocol every single day, is a challenge for many. This is one place where having healthy, personalized, fresh meals delivered to you is a huge benefit, and is a reason I partner with Square Fare. Having meals prepared to the specific restrictions of their current protocol, with no hidden ingredients and no cross-contamination risk, reduces a huge amount of friction for my clients. Square Fare's kitchen is entirely gluten-free, which alone eliminates one of the most common sources of unintended exposure for patients on elimination protocols.
Phase 2: Gut healing
While triggers are removed, the focus shifts to supporting the gut environment itself, its microbiome composition, intestinal lining integrity, and systemic inflammation. I use a food-first approach, with targeted supplemental support where appropriate to kickstart healing. I also address thegut-brain axis during this phase: chronic stress directly disrupts gut motility, barrier function, and immune regulation, which means stress management is part of the protocol, not optional.
One underappreciated way to reduce the stress load during this phase is eliminating the cognitive burden of meal planning and preparation. When patients aren't spending mental energy figuring out what they can eat, when that's already handled, they show up to the rest of their day differently.
Phase 3: Strategic reintroduction
Reintroduction is the phase most often rushed, skipped, or poorly executed. Foods are reintroduced one at a time, at controlled intervals, with careful symptom tracking and follow-up stool testing to confirm that clinical improvements are being reflected in the data. Reintroducing dairy, for example, means testing a single dairy-containing meal, not resuming dairy across all meals simultaneously. That's where the tailoring that Square Fare offers becomes particularly important. I can request one dairy-containing dinner in a week's meal plan, and this controlled, specific exposure is what allows me to interpret the response clearly. If something changes, I know exactly what caused it.
It's also worth noting that sensitivity is not always binary. A patient may react to raw broccoli but tolerate cooked broccoli. They may react to cow's milk but not almond milk. Preparation method, serving size, and food form all factor into the clinical picture. The ability to request specific preparation details (are the nuts roasted? can we test this ingredient in a cooked form?) is something I rely on regularly when working with patients through Square Fare.
Five practical tips for managing food sensitivities in daily life
1. Read labels carefully and consistently. Hidden ingredients are everywhere. Gluten appears in sauces, marinades, and products that don't appear to contain it. Soy is widespread in processed foods. Eggs appear in most baked goods. Consistent label reading is non-negotiable for anyone managing active restrictions. The habit needs to extend beyond packaged foods to restaurant menus, condiments, and snacks.
2. Keep meal composition simple. Complex meals with many ingredients make it difficult to isolate reactions during elimination and reintroduction phases. Simpler plates with fewer components are easier to track and easier to replicate when a meal is well-tolerated. This is a principle I apply throughout protocols with my patients, and it's part of why meals designed specifically for people with restrictions, rather than adapted from standard recipes, tend to work better clinically.
3. Prioritize nutritional adequacy. Food restriction without attention to nutritional completeness leads to deficiencies that worsen gut function, immune regulation, and energy — creating a cycle that slows recovery. Research published in theJournal of the Academy of Nutrition and Dietetics consistently supports the relationship between nutritional adequacy and immune function. Eating enough of the right foods is as important as avoiding the wrong ones.
4. Ask specific questions at restaurants. Cross-contamination is one of the most underestimated sources of accidental exposure. Shared cooking surfaces, sauces with unlisted ingredients, and menu changes all introduce risk. Asking direct questions such as "does this dish contain gluten?" or "is there dairy in the sauce?" is always appropriate. For patients in the elimination phase, the safest option is a kitchen that controls for allergens at the preparation level, which is why I often recommend Square Fare specifically during this period. The gluten-free kitchen environment removes an entire category of cross-contamination risk that restaurants can't reliably eliminate.
5. Plan your meals and snacks in advance. Having meals accounted for before the week begins is one of the highest-leverage things a patient can do for protocol adherence. Decision fatigue and unplanned hunger are two of the most common reasons people deviate — and under a food restriction protocol, an unplanned meal almost always means an off-protocol meal. When five lunches are handled through Square Fare, the only active decisions left are breakfast and dinner. My patients also love Square Fare's snacks specifically for this reason. Having a reliable, safe snack option available during a busy workday means one fewer moment where hunger and inconvenience can override a carefully constructed plan. That planning extends the reach of the clinical work I'm doing in sessions into the hours between them.
How I collaborate with Square Fare to support my clients
Most patients are surprised by how much coordination happens behind the scenes between my clinical protocol and what they're actually eating. When I'm working with Square Fare on a complex elimination and reintroduction protocol, I provide Claire with macronutrient targets such as specific grams of protein, carbohydrates, and fat per meal alongside the full restriction list and phase-specific modifications.
Square Fare's team then maps every meal against theUSDA FoodData Central database, uses in-kitchen technology to portion accurately to each client's profile, and executes those specifications every single week. The patient's role, at the end of all that, is to take the meal out of the fridge and heat it for two minutes.
That simplicity, especially in the context of a medically complex nutritional protocol, helps make compliance possible and takes a huge mental load (not to mention time and energy) off my clients plate. Patients who know their meals are handled, who aren't spending daily mental energy navigating their restrictions, are empowered to follow through with their protocols, which is then what I see reflected in their retesting data and in how they feel.
A clinical example: from food fear to recovery
One patient came to me after completing a comprehensive allergy panel with an allergist. The results were extensive. She had eliminated so many foods that by the time we met, she was going most of the day without eating, and surviving on chicken fingers at dinner because they felt reliably safe.
The clinical picture was severe under-nourishment compounded by food fear. The allergy panel had restricted her diet without resolving her symptoms.
We began with a stool test to establish a baseline of gut inflammation, then initiated a structured elimination protocol. Square Fare provided her meals that were nutritionally complete, limited in ingredients, safe for her current restrictions, and genuinely varied week to week. Within weeks, she was eating more food, more variety, and more vitamins and minerals than she had in a long time. Her energy improved as the direct result of being adequately nourished.
As her gut healed, we began systematic reintroduction. Eggs had been a significant trigger. After the healing phase, she tolerated them without reaction. That outcome was meaningful: eggs appear in almost every baked good, every restaurant menu, and most home cooking. Regaining access to them opened up her entire food world.
Conclusion
Food sensitivities are frequently not permanent. When symptoms are driven by underlying gut inflammation, and when that inflammation is addressed through a structured, evidence-based approach, many patients are able to reintroduce foods they believed they had lost. This is not universal, and it cannot be guaranteed. But it is common enough that it should be the working assumption at the start of treatment, not the exception.
The goal is always symptom resolution confirmed by clinical data: reduced inflammatory markers on follow-up stool testing, resolved symptoms, and successful reintroduction of previously reactive foods. When all three align, that is the outcome this approach is designed to produce.
If you're holding a panel result right now and feeling overwhelmed by what it's telling you to cut out, know that the list is a starting point, not necessarily a permanent restriction. Working with a licensed professional such as a registered dietitian can help you navigate exactly this.
Kendra Bova, MS, RDN, CDN, IFNCP is a Functional Registered Dietitian Nutritionist practicing virtually across New York, specializing in gut health, food sensitivities, hormonal health, and integrative nutrition.kendra-bova-nutrition.com
This post is based on a conversation from theFed by Science podcast, hosted by Claire Goldwitz, founder of Square Fare — a New York City meal delivery service that prepares fresh, personalized meals built around each client's exact macros, dietary restrictions, and health goals. Every meal is made from scratch, portioned individually, and ready in two minutes.getsquarefare.com — use code CHERRY for 20% off your first order.
