Functional dyspepsia: relieving indigestion by addressing root causes
Indigestion, discomfort, and fullness after eating can signal imbalances in digestion. The functional medicine approach addresses the root causes - improving stomach function, gut motility, and overall digestive health.
Natural treatment for indigestion and functional dyspepsia
Are you looking for safe and effective natural remedies for indigestion and functional dyspepsia? This page covers:
At Melbourne Functional Medicine, we’ll work with you to identify the root cause of your indigestion and functional dyspepsia to treat the real issue naturally and effectively, using our award winning approach to healthcare.
What is functional dyspepsia?
Understanding your condition
Functional dyspepsia is the presence of recurring indigestion symptoms with no clear cause. The symptoms include feelings of fullness with even a small meal, and a burning or gnawing sensation in the stomach area around the upper abdomen which can occur at any time, not just meal times.
Functional dyspepsia disrupts all aspects of life and is common in Australia, affecting around 1 in 10 people, and more women than men. It is also referred to as nonulcer dyspepsia or nonulcer stomach pain, and is the most common form of discomfort in the upper abdominal area.
What is functional dyspepsia?
Understanding your condition
Functional dyspepsia is the presence of recurring indigestion symptoms with no clear cause. The symptoms include feelings of fullness with even a small meal, and a burning or gnawing sensation in the stomach area around the upper abdomen which can occur at any time, not just meal times.
Functional dyspepsia disrupts all aspects of life and is common in Australia, affecting around 1 in 10 people, and more women than men. It is also referred to as nonulcer dyspepsia or nonulcer stomach pain, and is the most common form of discomfort in the upper abdominal area.
Functional dyspepsia, taking a deeper look
Often misdiagnosed, functional dyspepsia is suspected as a result of intestinal inflammation, sometimes developing following gastroenteritis. Potential underlying triggers can include Helicobacter pylori infection, altered motility (the transit of food) through the stomach and duodenum, an inability of the stomach muscles to relax when eating, and/or disrupted upper digestive tract gut flora.
Differentiating functional dyspepsia from conditions like gastro-oesophageal reflux disease (GORD/GERD), irritable bowel syndrome (IBS), or other digestive disorders requires careful investigation, as symptoms often overlap. Using detailed case histories and targeted functional testing, our practitioners focus on uncovering the root cause of your digestive symptoms and designing a personalised, evidence-based plan to restore gut health.
Functional dyspepsia symptoms
Discomfort and pain to the chest or upper abdominal area may have a diverse range of potential causes. Conditions of the heart and respiratory system should be ruled out first, and if pain is acute or there is any doubt, medical assistance should be sought immediately.
The symptoms of functional dyspepsia can be intermittent, long-lasting, and may include:
- Epigastric burning or pain in the mid to upper abdomen/stomach area, below the sternum that may be unrelated to meals, sometimes relieved by eating
- Early satiation – feeling full after a small meal
- Lack of appetite
- Nausea
- Bloating
- Belching
Functional dyspepsia is divided into two common presentations, based on symptoms and in the absence of any another condition providing an explanation:
Postprandial distress syndrome – where feeling full and/or unable to eat after a small meal, often resulting in discomfort, nutritional deficiencies and weight loss.
Epigastric pain syndrome – burning in the mid-upper abdomen 1 day per week in the past 3 months, for at least 6 months, not necessarily after eating. May be relieved by eating.
It is common for functional dyspepsia to be present alongside IBS, and GORD/GERD with symptom overlap, making teasing out the diagnosis difficult.
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Causes of functional dyspepsia
What causes functional dyspepsia in Australia? The statistics are similar to the rest of the Western world with up to one-third of the population experiencing recurrent gastrointestinal symptoms without signs of structural change to the oesophagus, stomach or upper intestines. A single cause for functional dyspepsia is unclear, however there are a number of risk factors known to contribute to its development:
- Being female
- Stress, anxiety, psychological distress, or a history of trauma that disturbs the gut-brain axis, affecting motility(transit time of food), digestion, gastric emptying and gut flora
- Slow gastric emptying
- Acute gastroenteritis infection – bacterial, viral or protozoan, including H. pylori
- Upper gastrointestinal system inflammation
- Dysbiosis of the upper small intestinal microbiome
- Impaired stomach muscle relaxation
- Inflammation of the duodenum
- Smoking
- Dysbiosis of oral microflora
- Use of non-steroidal anti-inflammatory drugs (NSAIDs) such as aspirin, Advil, Motrin, ibuprofen
- Presence of IBS, or GORD/GERD symptoms
- Alterations to the mucosal lining of the gut
- Heightened sensitivity to sensation in the gut (visceral hypersensitivity)
Functional dyspepsia treatment – the conventional approach
Conventional treatment of functional dyspepsia in Australia may take a number of consultations to establish a diagnosis, due to overlap of symptoms with other conditions. To establish this diagnosis, your GP will review your symptoms and make a physical examination. Various blood tests, H. pylori testing and X-ray may be required.
Initially ruling out heart or respiratory conditions, you may also require an endoscopy, where a small, flexible camera is passed down the oesophagus into the stomach and upper small intestines. An endoscopy may identify damage to the oesophagus, stomach or upper intestines indicating conditions such as gastric or peptic ulcers, oesophagitis or GORD/GERD. An endoscopy must be conducted if any of the following are present:
- Signs of anaemia or bleeding in the digestive system
- Vomiting
- Worsening of symptoms
- Previous gastric surgery
- Unexplained weight loss
- Over 55 years
- Difficulty in swallowing
- Family history of stomach cancers
Once functional dyspepsia has been identified, medication may be prescribed, such as:
- Proton pump inhibitors (PPIs)– such as Somac, Nexium, Prilosec, and Prevacid which reduce the amount of acid secreted by stomach cells. Manufacturers recommend that PPIs are not taken longer than 14 days in a cycle and for no longer than 3 months total. Side effects can include poor digestion and absorption of nutrients
- H2 receptor antagonists – these inhibit the production of gastric acid. Side effects can include poor digestion and absorption of nutrients
- Prokinetic drugs – which stimulate the stomach to empty more rapidly
- Over-the-counter antacid medicines such as Gaviscon which neutralise acid, inhibiting digestion and absorption of nutrients
- Fundic relaxors – such as Cisapride or the anti-anxiety drug buspirone, to relax stomach muscles
- Low-dose tricyclic antidepressants such as amitriptyline
- Antibiotics – such as rifaximin, which are non-selective antimicrobial agents that kill both beneficial and detrimental species alike, and disrupt the gut flora diversity and makeup
These medications have side effects and can contribute long-term to poor digestion, nutrient depletion and disrupted gut flora, triggering other digestive symptoms, and are generally not recommended long-term.
Other treatment strategies include:
- Counsellor or therapist referral for behavioural therapy to help cope with symptoms that medication cannot relieve
- Some dietary recommendations may be made, such as eating smaller, low-fat meals, eliminating wheat, carbonated drinks, fatty, and fried or spicy foods
A 2016 study identified that current conventional treatments for functional dyspepsia are ‘largely unsatisfactory’. This is why many people with functional dyspepsia are looking for long-term, natural solutions to their digestive discomfort.
Functional dyspepsia treatment – the functional medicine approach
Functional dyspepsia natural treatment can be very effective, safe and long-lasting. Using evidence-based methods within a holistic framework, our functional medicine practitioners have a unique approach to all digestive conditions. The first step involves isolating the root cause of the symptoms with detailed investigations of:
- Symptoms and signs
- Your family history and genetic susceptibility
- Digestive function history
- Detailed personal medical history
- Travel, specific illness and symptom history
- Medications, supplementation
- Diet and lifestyle
- Environmental exposures
Functional testing may help identify pathogens, parasites and infections, such as H. pylori using state-of-the-art pathology labs. These tests may include:
- GI Map or, GI 360 – state of the art testing isolating via DNA PCR, a far more accurate test than culturing.
Other functional testing may be required to identify:
- Food allergy/intolerances
- Nutrient deficiencies
- Gut dysbiosis / IBS / SIBO, other suspected conditions
Natural treatments for indigestion will vary according to the underlying causes, but may include:
- Stimulating vagus nerve tone which has been recognised as an effective treatment for functional dyspepsia. Measuring heart rate variability can be indicative of the effectiveness of this strategy, as the vagus nerve serves both digestive and cardiac system functions
- Lifestyle medicine such as stress resilience techniques – meditation, mindfulness, shinrin-yoku (forest bathing) and breathwork
- Strategies to improve sleep, quit smoking, alcohol, and decrease weight
- Dietary recommendations – to eliminate food intolerances, trigger foods and improve nutrient status
- Supplements to promote healthy digestion such as betaine hydrochloride, digestive enzymes, slippery elm powder, fibre supplements
- Supplements for mucosal repair such as zinc, Vitamin A, Vitamin C, magnesium and glutamine
- Herbal medicines for mucosal repair/anti-inflammatories – meadowsweet, calendula, licorice, turmeric, marshmallow, aloe
- Herbal antacids such as meadowsweet, slippery elm powder, and alfalfa
- Digestive stimulants to improve gastric emptying (used with caution) – gentian & ginger
- Anti-pathogenic herbs such as pomegranate husk, garlic, turmeric, and berberine
- Other herbs as required e.g. anti-anxiety, mood modulation, detoxification, bile production and tone/repair of gastric muscles and mucosal linings
- Precision probiotics to facilitate a diverse and healthy microbiome
- Fibre supplementation (prebiotics) to maintain a healthy microbiome and enhance digestive emptying
At Melbourne Functional Medicine, our practitioners are familiar with all kinds of digestive disorders and have effective, natural and safe treatment strategies to help you find the relief you are looking for. All-natural treatments for indigestion are personalised to treat the whole person, and will consider and address other conditions or symptoms you may be experiencing.
Our unique program gives you ongoing support from your own practitioner and health coach team to get you well again. Making the changes necessary to improve health can be hard, so having your own health coach to inspire, educate, empower and support you can help you achieve wellness quicker and easier than doing so alone. It is this revolutionary approach to your health that gets results for many Australians like you. Read our success stories for more information.
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Frequently
Asked
Questions
What causes indigestion?
Indigestion can be triggered by a wide range of factors, including:
- Digestive disorders such as reflux, IBS, or ulcers
- Side effects of certain medications
- Food intolerances or sensitivities
- Stress and nervous system imbalance
- Disrupted gut microbiome
- Slow transit time of food through the digestive tract
- Gut infections or parasites
If symptoms are ongoing and no clear cause is found, the condition may be referred to as functional dyspepsia. This is where detailed assessment and investigation can help uncover underlying drivers.
What does indigestion feel like?
Indigestion describes discomfort or pain in the mid-upper abdomen, often with a burning sensation. Symptoms vary from person to person, but may include:
- Nausea or queasiness
- Burping or belching
- Vomiting
- Reduced appetite
- Feeling full after only a small meal (early satiety)
Because indigestion can have many different causes, a thorough assessment is often needed to clarify what’s driving your symptoms.
How do I get rid of indigestion? Why won’t my indigestion go away?
The best way to relieve indigestion depends on the underlying cause. Common drivers include:
- Gastro-oesophageal reflux disease (GORD/GERD)
- Functional dyspepsia
- Irritable bowel syndrome (IBS)
- Small intestinal bacterial overgrowth (SIBO)
- Food intolerances
- Parasitic infections
- Microbiome imbalances
Short-term strategies that some people find helpful include:
- Herbal teas: ginger, chamomile, or lemon balm
- Soothing supplements: slippery elm powder
- Lifestyle support: eating slowly, smaller meals, and reducing stress
While these may ease discomfort, lasting relief usually comes from addressing the root cause. A functional medicine practitioner experienced in digestive health can investigate in detail and create a tailored, evidence-based treatment plan.
What does burping after eating mean?
Burping after eating usually means gas is building up in the stomach or upper digestive tract. This can happen for many reasons, including:
- Eating quickly and swallowing excess air
- Stress or anxiety
- Food intolerances or sensitivities
- Gastro-oesophageal reflux disease (GORD/GERD)
- Acid reflux
- Small intestinal bacterial overgrowth (SIBO)
- Irritable bowel syndrome (IBS)
- Microbiome imbalances
- Functional dyspepsia
Because burping can be linked to several digestive conditions, understanding the cause often requires detailed investigation. At Melbourne Functional Medicine, our practitioners combine many years of clinical experience with state-of-the-art functional testing to identify the root cause of your symptoms. This evidence-based, science-driven approach means we can design personalised strategies that aim for lasting relief, not just temporary fixes.
What is the best way to sleep with indigestion?
Changing how and when you eat, along with a few simple strategies, can sometimes ease indigestion at night. Helpful approaches include:
- Meal timing: Eat smaller meals, finishing at least 3 hours before lying down
- Herbal teas: Ginger, chamomile, lemon balm, licorice, or peppermint teas may calm the digestive system
- Soothing supplements: 3 tsp of slippery elm powder mixed in water can help coat the digestive tract and support microbiome health. Stay well hydrated if taking fibre-based supplements
- Sleep position: Elevating the head of the bed or mattress can reduce symptoms that worsen when lying flat
For ongoing or persistent indigestion, working with a functional medicine practitioner experienced in dyspepsia and digestive health can provide clarity. By identifying the root cause of your symptoms, they can develop a clear and personalised treatment strategy for long-term relief.
Does stress cause heartburn and indigestion?
Yes. Chronic stress can significantly affect digestion, even if we don’t always recognise we’re under stress. Everyday pressures such as work, money, family, traffic, or noisy environments can keep the body in a low-level stress state.
When this happens, the sympathetic nervous system (SNS) – the “fight or flight” response – is activated. This stress state prioritises survival functions like blood flow to the muscles and brain, while reducing digestive activity, including:
- Lower saliva and digestive juice production
- Reduced movement of food through the digestive tract
- Increased sensitivity in the gut lining
These changes slow digestion and can result in symptoms such as heartburn, indigestion, bloating, or discomfort after meals.
If stress-driven indigestion or heartburn is frequent, working with a functional medicine practitioner experienced in digestive health can help identify the link between nervous system patterns and gut function, and guide you toward strategies for long-term relief.
Can exercise help with indigestion?
Yes. Exercise can support digestion by stimulating the intestines to move food along (peristalsis), which helps waste elimination and improves bowel movement frequency. This is especially helpful when indigestion is linked to constipation or slow motility.
When motility slows, it can alter the gut microbiome and digestive environment, increasing the risk of conditions such as reflux, indigestion, functional dyspepsia, IBS, or SIBO. Regular movement helps counter this process.
Other measures that can support digestive health include:
- Drinking at least 2 L of clean water daily
- Practising meditation, yoga, Tai Chi, or mindfulness to improve stress resilience
- Eating a variety of whole, unprocessed fruits and vegetables each day
For ongoing or persistent indigestion, working with a functional medicine practitioner experienced in digestive health can help uncover whether slow motility, constipation, or other factors are contributing, and provide a personalised, evidence-based plan for relief.
What is functional dyspepsia?
Functional dyspepsia could be described as indigestion pain in the chest, or upper abdomen that occurs without any apparent cause. It is sometimes referred to as non-ulcer stomach pain. Symptoms usually include:
- Feeling full after eating a small or regular meal (early satiety)
- Lack of appetite
- Burping
- Belching
- Nausea
- Burning, gnawing pain or sensation to the mid-upper abdomen
Once all other explanations have been ruled out, such as cardiac pain, acid reflux (GORD/GERD), gastritis, IBS, IBD, SIBO, seeking a functional dyspepsia natural treatment will help to resolve symptoms for good.
Functional medicine treatment of functional dyspepsia will identify the root cause of the symptoms and treat them accordingly. Natural remedies for indigestion and digestive disorders can be safe, effective and give you back your health.
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