Restrictive diets are often introduced with good intentions. Many people arrive at approaches like low histamine, low FODMAP, low carb or highly limited food plans because they are genuinely unwell. Symptoms such as bloating, pain, reflux, rashes, fatigue, anxiety or bowel changes can be overwhelming, and removing foods can feel like the only way to regain some sense of control.
And in the short term, these diets can absolutely help. Symptoms may reduce. The gut may feel calmer. Life may become more manageable.
The problem arises when a diet designed as a temporary therapeutic tool quietly becomes a long term way of eating. Over time, this can shift the gut environment in ways that actually increase inflammation, sensitivity and disease risk, even if symptoms initially appeared to improve.
In this blog, we discuss the hidden risks of long-term restrictive diets and why long-term healing requires more than ongoing food restriction.
Why restrictive diets are meant to be short-term
Most elimination diets are not designed to be nutritionally complete or microbiome supportive when followed indefinitely. They are intended to reduce symptoms temporarily while the underlying drivers of gut dysfunction are addressed.
When restriction continues without a clear reintroduction plan, the gut microbiome begins to change. Diversity reduces. Beneficial bacteria struggle to survive. The gut lining becomes more vulnerable. Over time, the very systems we rely on for digestion, immune balance and tolerance can become weaker rather than stronger.
This is particularly relevant for diets that significantly reduce fibre intake, like low FODMAP, low carb, Atkins or carnivore. I speak about this without judgment as I have been there myself! I was stuck on just a handful of foods. Restricted diets are not only limiting from a social, flavour and enjoyment perspective. It can lead to more gut dysfunction, symptoms and pain.
Fibre, bacteria and the gut lining
Dietary fibre is not just about bowel movements. Fibre is the primary fuel source for many beneficial gut bacteria (a prebiotic). When these bacteria ferment fibre, they produce short-chain fatty acids such as butyrate.
Butyrate plays a critical role in gut health. It helps maintain the integrity of the gut lining, reduces inflammation, supports immune regulation and even influences nervous system signalling between the gut and brain.
When fibre intake drops too low for too long, butyrate-producing bacteria begin to decline. As their preferred fuel disappears, some bacteria adapt by turning to alternative energy sources. One of these sources is the mucus layer that protects the gut lining.
Over time, this can thin the mucus barrier, leaving the gut more exposed, more reactive and more prone to inflammation. This can increase gut permeability (aka leaky gut), and contribute to increased food sensitivities rather than resolving them!
For those with Histamine intolerance, understanding how to feed your gut bacteria without causing a histamine flare-up, is a key focus. Read more here.
The low FODMAP example
Low FODMAP is one of the clearest examples of a diet that works well short-term but can cause problems long-term if not properly managed.
In the elimination phase, fermentable carbohydrates are reduced to decrease gas production and gut distension. This can be extremely helpful for symptom relief, particularly in people with IBS or SIBO.
However, many of the foods restricted on a low FODMAP diet are also rich sources of prebiotic fibre. These fibres selectively feed beneficial bacteria, including those involved in butyrate production.
Research has shown that following a low FODMAP diet long-term can significantly reduce populations of beneficial gut bacteria. Without reintroduction and diversification, the gut ecosystem becomes less resilient. In some cases, food tolerance worsens over time, leading to an increasingly narrow diet and greater fear around eating.
Over time, staying in the elimination phase can create new issues rather than resolving the original ones.
Low fibre, meat-heavy diets and inflammation
Another growing concern relates to long-term low-fibre, high-protein or meat-heavy diets. These patterns can shift the microbiome toward bacteria that produce inflammatory metabolites.
One example is hydrogen sulphide-producing bacteria. In small amounts, hydrogen sulphide plays normal physiological roles. In excess, it can irritate the gut lining, impair mitochondrial function in gut cells and contribute to inflammation. This type of bacteria typically loves to eat saturated fats and meat, so in a meat-heavy diet, they flourish.
Low fibre intake appears to encourage the growth of these bacteria while reducing populations that help maintain gut barrier integrity. This imbalance can increase gut sensitivity and may play a role in chronic digestive symptoms.
There is also emerging evidence linking long-term low-carbohydrate or highly restrictive dietary patterns with increased bowel cancer risk. Large meta-analyses of prospective cohorts show higher colorectal cancer risk with more red and processed meat. Some studies suggest that risk may increase within several years of sustained low-fibre intake, particularly when diets are low in plant diversity and resistant starch.
While research in this area continues to evolve, it reinforces a principle we already understand well. The gut thrives on variety, fibre and balance over time.
Why grains and plant diversity matter
Grains are often one of the first food groups removed in restrictive diets. For some people, this can be helpful in the short term. When used for 6-10 weeks during treatment for IBS or SIBO, it can help reduce symptoms, but long-term avoidance can reduce important fibre sources and limit microbial diversity.
Whole grains provide fermentable fibres, resistant starch and polyphenols that support beneficial bacteria. When tolerated, they can play a valuable role in gut and metabolic health.
Beyond grains, plant diversity is one of the strongest predictors of a healthy microbiome. Research suggests that consuming around 30 different plant foods per week is associated with greater microbial diversity and improved overall health outcomes. I usually recommend aiming for 30-40 different plant foods across each week, including herbs and spices, to feed our good gut bacteria and give our body the nutrients it needs to fight inflammation.
These plant foods include vegetables, fruits, legumes, nuts, seeds, herbs, spices and whole grains. Diversity matters more than perfection. Each plant provides slightly different fibres and phytonutrients, feeding different microbial populations.
A narrow diet, even if it feels safe, limits this diversity and reduces the gut’s ability to adapt.
Where low histamine fits in
Low histamine diets can be extremely helpful for people with histamine intolerance, mast cell activation or nervous system-driven histamine sensitivity. Reducing histamine load can provide much needed symptom relief while the drivers of intolerance are addressed.
However, low histamine diets are not intended to be lifelong. Many low histamine food lists significantly reduce fermented foods, leftovers, types of fish, certain fruits, vegetables and grains. Over time, this can unintentionally lower fibre intake and plant diversity.
Staying on a highly restricted low histamine diet for months or years without progression can increase the risk of gut dysbiosis, nutritional gaps and increased food fear.
The long-term goal is not avoidance. The goal is improved tolerance, nervous system regulation and a more resilient gut that can handle a wider range of foods with fewer symptoms.
A better long-term approach
Rather than asking which diet to stay on forever, a more helpful question is how to use dietary tools strategically.
Elimination phases should be time limited and purposeful. Reintroduction should be gradual, supported and individualised. The focus should shift from restriction to building tolerance, diversity and resilience.
This often involves addressing factors beyond food, including gut inflammation, microbiome balance, nutrient status, stress physiology and nervous system regulation. Food reactions are rarely just about the food itself!
Get help with your low histamine diet
Working with a practitioner can help ensure that dietary changes support healing rather than unintentionally creating new problems. Having a plan to treat the root causes of the symptoms and reintroduce is key.
Healing the gut is not about finding the perfect diet. Or about killing ALL the bacteria. It is about creating an internal environment that is flexible, supported and adaptive. Feeding the “good guys” brings everything into balance and naturally suppresses overgrowth of the “bad guys”.
Short-term dietary restriction can be a valuable part of that process. Long-term restriction without progression can move us further away from true gut health and lead to more symptoms, more pain and more problems.
If you feel stuck on a restrictive diet or are reacting to more foods over time, it may be a sign that the risks of long-term restriction are beginning to outweigh the benefits, and that your body is ready for the next phase of healing. Food should be about joy and connection. It should support nourishment, confidence and resilience over time, not ongoing fear and limitation. We can help you get your gut back into good working order and shift from this stuck phase back to food freedom. Watch my free Masterclass to find out how you can get rid of the food sensitivities and enjoy eating a wide range of foods again.
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Watch my free Masterclass – the 5 secrets to healing from histamine intolerance.
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References
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Interstitial Cystitis and Histamine Intolerance