Food processing plays a central role in modern food systems, shaping everything from safety and shelf life to taste and convenience. However, the way food is handled, from harvest to packaging, can significantly alter its nutritional value. While some methods preserve or even enhance nutrients, others strip away fibre, vitamins, and bioactive compounds, contributing to poor dietary quality. As ultra-processed foods dominant global diets, understanding the health implications of different processing techniques is essential for informed choices, public health advocacy, and sustainable food system reform.

Agricultural and Processing on Nutritional Quality

Biological and chemical processes in agriculture play a major role in shaping soil health and by extension, the nutritional quality of the crops we eat. Intensive farming and widespread use of synthetic pesticides may help reduce crop loss, but they can also disrupt soil microbial communities. Over time, this leads to soil degradation and weaker nutrient cycling, making it harder for plants to absorb essential micronutrients. While direct links between soil microbes and human health are still being studied, there’s growing evidence that healthy, biodiverse soils produce more nutrient-rich crops, which support better overall nutrition.

Biofortification enhances the nutrient content of crops through breeding or soil treatments and has shown promise for micronutrients like zinc and selenium. Iron remains more challenging due to absorption issues and soil interactions. However, new techniques using genetic engineering and microbial inoculants are helping to improve iron uptake, especially in staple crops like beans and rice. Biofortification is cost-effective, but its success depends on soil conditions, crop type, and whether consumers accept the changes.

Regenerative agriculture is gaining attention for its ability to restore soil health and boost crop nutrition. Practices like cover cropping, composting, and reduced tillage have been shown to increase levels of vitamin C, zinc, and beneficial plant compounds such as polyphenols and antioxidants. These compounds are increasingly recognised for their role in reducing inflammation and supporting immune health.

Processing methods after harvest also affect nutritional value. Techniques like milling, refining, and high-heat treatment can strip away fibre, vitamins, and bioactive compounds reducing the health benefits of otherwise nutritious foods. On the other hand, methods like fermentation and sprouting can improve nutrient absorption and reduce anti-nutrients that interfere with digestion.

Altogether, soil health, farming practices, and food processing form a complex but vital foundation for food safety and nutrition. As research continues to evolve, adopting sustainable and regenerative approaches offers an alternative way to improve both human health and the health of the planet.

How Processing Affects What We Eat and What We Absorb

Food processing covers every stage from harvesting and storage to manufacturing, packaging, and distribution. Whether chemical, biological, or physical, these methods aim to improve food safety, extend shelf life, and maintain or enhance nutritional quality. Common techniques include fermentation, freezing, irradiation, pasteurisation, smoking, and canning.

Primary processing involves minimal steps like washing, cutting, or pasteurising milk, preparing raw foods for consumption or further transformation. Secondary processing goes further, turning raw or lightly processed ingredients into new forms, such as extracting oils or refining grains. Foods that undergo multiple stages and include additives like emulsifiers, preservatives, or artificial flavours are classified as ultra-processed foods (UPFs). Examples include packaged cakes, ready meals, and sugary cereals.

While processing can help preserve nutrients and prevent spoilage, methods used in UPFs often raise health concerns. These foods tend to contain high levels of salt, sugar, and saturated fats, which contribute to excessive calorie intake and increase the risk of obesity, heart disease, and type 2 diabetes. Some additives and industrial techniques may also alter the food’s structure in ways that affect digestion, satiety, and gut health.

The Scientific Advisory Committee on Nutrition (SACN) in the UK recently reviewed the evidence and found that higher consumption of UPFs is linked to poorer health outcomes, although the exact mechanisms are still being explored. Importantly, not all UPFs are unhealthy, some, like certain oat and nut bars, can still offer good nutritional value, but most are energy-dense and low in essential nutrients.

New non-thermal processing technologies such as high-pressure processing, pulsed electric fields, cold plasma, and UV-C treatment are gaining attention. These methods help preserve heat-sensitive nutrients like vitamins and antioxidants while ensuring food safety without relying heavily on additives. They also support cleaner labels and more sustainable production practices.

Preserving micronutrients during processing is especially important in regions where deficiencies in iron, vitamin A, and zinc are common. Careful handling and storage help prevent spoilage and contamination from environmental or microbial toxins, which can lead to illness and further nutrient loss.

How Toxins Enter Our Diet

Toxins can enter the food supply through various routes including environmental contamination, microbial growth, agricultural residues, natural compounds, and intentional additives. These exposures can occur at any stage of the food system, during farming, processing, packaging, cooking, or storage.

• Microbial contamination remains one of the most serious threats. Harmful bacteria such as Salmonella, Listeria, and E. coli, along with moulds that produce mycotoxins, pose significant risks. Viruses like Hepatitis A can also be transmitted through contaminated food, as seen in outbreaks linked to frozen berries.

• Environmental contaminants including heavy metals like arsenic, lead, cadmium, and mercury, as well as industrial chemicals and PFAS (per- and polyfluoroalkyl substances) can accumulate in soil, water, and air. These toxins may enter crops and livestock, posing particular risks to vulnerable groups such as children and pregnant women.

• Agricultural residues from pesticides and veterinary drugs can persist in non-organic meat and produce. For example, arsenic-based drugs once used in poultry production have raised health concerns, although many have been phased out in regulated markets. Organic farming standards prohibit synthetic pesticides and medications, helping reduce toxic exposure.

• Organic farming does allow certain pesticides, but only those derived from natural sources like plant oils, minerals, or microbes. These tend to be less toxic and less persistent than synthetic alternatives, though they can still affect soil health and non-target organisms if overused.

• Cooking methods can also generate harmful compounds. High-temperature techniques such as grilling, frying, or roasting can produce heterocyclic amines (HCAs) and polycyclic aromatic hydrocarbons (PAHs) known carcinogens found in the muscle tissue of meat and fish.

• Naturally occurring toxins include solanine in green potatoes, cyanogenic glycosides in cassava, and lectins in undercooked legumes. These are usually neutralised through proper cooking and preparation.

• Microplastics and nanoplastics may enter food through packaging or environmental exposure. While their long-term health effects are still being studied, they are increasingly recognised as a potential risk.

Given these multiple entry points, accurate food labelling, safe cooking practices, and regulatory oversight are essential to minimise exposure and protect public health.

Food Labelling for Safer Choices

Food labelling in the UK plays a vital role in protecting public health, enabling informed choices, and ensuring legal compliance. Labels must include key information such as ingredients, allergens, use-by dates, storage instructions, and nutritional content, as required by UK law and overseen by the Food Standards Agency (FSA). While the UK previously followed EU legislation, it now operates under its own food law frameworks. Recent updates such as the Food Law Practice Guidance 2025 and the Northern Ireland Retail Movement Scheme have introduced new labelling requirements, particularly for cross-border trade.

Loose foods, like fresh produce, are exempt from full labelling unless pre-packed, which can limit access to allergen and origin details. In contrast, pre-packed foods such as meat, fish, eggs, and spices must display full labelling, including allergen declarations and traceability information.

To help consumers interpret nutritional content more easily, the UK introduced the traffic light labelling system, which remains widely used. It highlights levels of fat, saturated fat, sugar, and salt using red (high), amber (medium), and green (low) indicators. This system has been shown to improve public understanding and encourage healthier choices, especially when paired with nutrition education.

While the traffic light system simplifies nutrition labels, it can oversimplify complex health information. It doesn’t account for portion size, overall dietary patterns, or the presence of beneficial nutrients like fibre or protein. Some ultra-processed foods may still receive green ratings despite being low in nutritional value, which can mislead consumers.

Ingredient transparency remains a challenge as manufacturers often use technical or unfamiliar names for additives and sweeteners, making it difficult for consumers to assess potential health risks. This can lead to unintentional overconsumption of sugar, salt, or preservatives, contributing to obesity and chronic disease. As a result, there are growing calls for simplified ingredient naming and digital labelling tools, such as QR codes that link to full ingredient explanations.

Recent studies show that while consumers increasingly prioritise quality and ingredient information over taste, many still struggle to interpret labels correctly. There’s a growing push for better public education on nutrition, especially around ultra-processed foods (UPFs). These products may meet labelling standards but still pose health risks due to their formulation and use of additives.

Finally, environmental and sustainability labelling including carbon footprint indicators and recycling instructions is becoming more common, reflecting rising consumer demand for ethical and eco-conscious choices.

Key Takeaways

• Nutrient Loss: Techniques like milling, refining, and high-heat treatment can strip away fibre, vitamins, and antioxidants

• Additive Overload: UPFs often contain high levels of salt, sugar, and saturated fats, contributing to obesity, heart disease, and type 2 diabetes.

• Food Matrix Disruption: Industrial processing can alter how food is digested and absorbed, affecting satiety and gut health

• Misleading Labels: Some UPFs may appear healthy due to favourable traffic light scores, despite being energy-dense and nutrient-poor.

• Traffic Light System: Helps identify fat, sugar, and salt levels, but may oversimplify health risks.