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Food Intolerance Explained: A Dietitian’s Guide to Managing Gut Symptoms

by Intoleran Australia

Food Intolerance Explained: A Dietitian’s Guide to Managing Gut Symptoms

Karina Savage APD-  Intoleran Dietitian

Sept 2025

Food is one of life’s greatest joys, but for many people it can also be a source of ongoing discomfort.

It is estimated that up to 25% of the Australian population believe they have a food intolerance (NSW Government Food Authority , 2025) .  Symptoms such as bloating, abdominal pain, urgent loose bowel actions, to skin rashes, headaches and fatigue.

Food-related symptoms are surprisingly common and often confusing. People often wonder whether they are caused by a food intolerance or a food allergy. It can be a super confusing arena, one which can be “mis managed” without the right guidance/advice.

This blog will discuss what food intolerance really is, how it differs from a food allergy, the common symptoms to look out for, the mistakes people often make when trying to “DIY” their way out of gut issues, and evidence-based strategies—including elimination diets like low FODMAP and digestive enzymes, that can actually help.

What is a Food Intolerance?

A food intolerance occurs when your body has difficulty digesting, processing or absorbing certain foods.

Unlike an allergy, which involves the immune system, food intolerances usually stem from the digestive system (otherwise known as your Gastro-intestinal tract).

Food Intolerance happens because the body either lacks a specific enzyme required to break down a component of food (often the carbohydrate component), or because certain chemicals or compounds in the food irritate the gut.

Some common examples include:

  • Lactose intolerance – due to reduced levels of the enzyme lactase, leading to difficulty digesting lactose (the sugar in milk).
  • Fructose intolerance – when the body struggles to adequately absorb fructose, a naturally occurring sugar in fruit, juice and honey.
  • Histamine intolerance – when people react to histamine-rich foods such as aged cheeses, wine, and cured meats, often due to low activity of the DAO (diamine oxidase) enzyme.

Food intolerances are often dose-dependent. This means that small amounts of the food might be tolerated, while larger amounts trigger symptoms.

How Food Intolerance Differs from Food Allergy

It is important to understand the difference between a food intolerance and allergy. The reason being, they have very different dietary approaches.

A food allergy involves the immune system and the body is reacting to the Protein in food. While food intolerance, involves the gastro-intestinal tract, and the body is reacting to the Carbohydrate in food.

A good way to think about it is: allergies are about the immune system overreacting, while intolerances are about the gut struggling.

Common Symptoms of Food Intolerances

Food intolerances can present with a wide range of symptoms. Some of the most common include:

  • Gastrointestinal: bloating, abdominal cramps, excessive wind, diarrhoea, constipation, nausea.
  • Skin: eczema flare-ups, rashes, hives.
  • Neurological: headaches, migraines, brain fog.
  • Systemic: fatigue, irritability, joint pain.

Because of the similarity of symptoms with allergies and intolerances, it’s easy to see why many people get confused. These symptoms are often vague, can appear hours after eating, and vary from day to day depending on stress levels, gut health, and even sleep.

Common strategies to improve Food Intolerance.

The symptoms of food intolerance can be quite debilitating, and for this reason  many people try to self diagnose and fix their symptoms as soon as possible. Here are common strategies trialled to improve food intolerance.

  1. Self-directed food elimination – The first instinct is usually to eliminate entire food groups (gluten, dairy, etc.), hoping to feel better. The risk with removing whole food groups is the increased risk of nutritional deficiency. Often with food intolerance, we don’t need to avoid whole food groups, we just need to reduce/avoid specific foods.
  2. Over-the-counter remedies – Antacids, laxatives, peppermint oil capsules, or probiotics are common first-line attempts. These can be a nice support to manage symptoms, but don’t address the underlying cause.
  3. Following online advice – Google searches and social media often lead people down super restrictive diets without proper guidance. The online world is filled with mis-information and is often contradicting, leaving people feeling very confused and overwhelmed. It can also increase the risk of an incorrect dietary approach, which can come with health risks.
  4. “Healthy eating” resets – Cutting out processed foods and alcohol is definitely a healthy approach and may also help with food intolerance. Having said this, it doesn’t necessarily address the underlying issue, therefore symptoms may persist.

While these approaches can sometimes bring partial relief, they often create new problems such as nutrient deficiencies, frustration, or even worsening gut symptoms.

Common mistakes people make when trying to manage food intolerance

When trying to self diagnose and manage on their own symptoms, there are some common mistakes can make the situation worse. They include:

1. Over-restriction of the diet

Cutting out too many foods without professional guidance can reduce dietary diversity. This may worsen gut microbiome health, which ironically increases food sensitivities.

2. Confusing intolerance with allergy

Parents in particular often panic when their child reacts to a food, assuming it’s an allergy when it may be intolerance. This can lead to unnecessary fear and avoidance of safe foods.

3. Using probiotics randomly

Probiotics are not “one-size-fits-all.” The wrong strain can worsen bloating or diarrhoea, and only a few strains are proven to be effective for helping irritable bowel like symptoms.

4. Not seeking medical advice

Symptoms of food intolerance can sometimes overlap with serious conditions such as coeliac disease, inflammatory bowel disease (IBD), or even bowel cancer. Self-diagnosis risks missing red flags.

Steps to best manage food intolerance.

Managing food intolerance requires an approach that’s safe, evidence-based, and personalised. Here are the steps that should be taken.

Step 1: Rule Out Other Conditions

If you are suffering with ongoing gut symptoms, it’s important to speak with your doctor to rule out an underlying conditions. Whilst rare, your doctor should rule out conditions such as Coeliac disease (an autoimmune reaction to gluten) and Inflammatory bowel disease (IBD) (Crohn’s or ulcerative colitis) or other.

Step 2: Keep a Symptom and Food Diary

Tracking what you eat and when symptoms occur can help identify patterns – especially if you go to see a Dietitian, this can be very helpful to show them. This isn’t about obsessing—it’s about gathering clues for a professional to interpret.

Step 3: Consider a Dietary Elimination Trial – The Low FODMAP Diet

The low FODMAP diet is the gold standard for managing Food Intolerance or Irritable Bowel-like symptoms. FODMAPs are fermentable carbohydrates found in many healthy foods (like onions, garlic, apples, beans). In sensitive individuals, they can cause gas, bloating, pain, and altered bowel habits (either constipation or diarrhoea).

The process involves three stages under the guidance of a Dietitian:

  1. Elimination phase (4–6 weeks): Temporarily restrict high-FODMAP foods under dietitian guidance.
  2. Reintroduction phase: Systematically reintroduce food groups one at a time to identify triggers.
  3. Personalisation phase: Build a long-term diet that includes as many foods as possible while keeping symptoms controlled.

It’s critical to note: low FODMAP is not meant to be a lifelong diet. Long-term restriction can starve the gut microbiome and create nutritional gaps. This is why working with a Dietitian is essential.

Step 4:  Lifestyle and Gut Health Support

Beyond food, other factors strongly influence Digestive Issues:

  • Stress management – The gut-brain axis is powerful; mindfulness, yoga, and breathing exercises can reduce symptoms.
  • Sleep quality – Poor sleep worsens gut sensitivity.
  • Physical activity – Regular movement helps regulate bowel function.
  • Gut microbiome support – A diverse, fibre-rich diet (once tolerated) helps rebuild a resilient gut.

Step 5: Digestive Enzymes as a Tool

For some intolerances, digestive enzymes can be very helpful. These supplements work by replacing or supporting the body’s natural enzymes. Examples include:

  • Lactase tablets – for lactose intolerance, allowing dairy to be consumed without symptoms.
  • Alpha-galactosidase – to help digest carbohydrates in beans and lentils.
  • Xylose Isomerase – to help digest fructose in fruit
  • Invertase – to help digest sucrose
  • Glucoamylase – to help digest starch
  • DAO supplements –used for histamine intolerance.

Whilst enzymes are not a cure-all, they can offer relief of symptoms and flexibility in certain situations – such as when eating out. 

Key Takeaways for Food Intolerance 

  • Food intolerances are digestive system issues, with symptoms such as bloating, cramps, constipation, diarrhoea, and fatigue.
  • Common mistakes include over-restriction, confusing allergy with intolerance, and self-diagnosing without professional input.
  • Evidence-based strategies include ruling out serious conditions, keeping a symptom diary, trialling a low FODMAP diet, and using digestive enzymes where appropriate.
  • Long-term success comes from personalised guidance from a Dietitian, not a generic “one-size-fits-all” approach.

Living with ongoing gut symptoms can be exhausting and uncomfortable, but the good news is that there are effective strategies available—that are backed by research and clinical experience. By understanding the difference between intolerance and allergy, avoiding the common traps of self-diagnosis, and working with the right professionals, it is absolutely possible to improve your gut health.

Food should fuel your body, not cause daily distress. With the right guidance, you can rebuild your confidence around eating, nourish your gut, and enjoy food again.

Karina Savage APD, Intoleran Dietitian

Sept 2025

REFERENCES

1.      NSW Government Food Authority, Allergy and intolerance [Accessed  1 Sept 2025]. Available from https://www.foodauthority.nsw.gov.au/consumer/life-events-and-food/allergy-and-intolerance.

 

2.      Misselwitz B, Butter M, Verbeke K, Fox MR. Update on lactose malabsorption and intolerance: pathogenesis, diagnosis and clinical management. Gut. 2019;68(11):2080-91

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