Four key areas of allergen cross-contact risk across the food supply network: Where risk starts and how to control it

18 June 2026 | Wendy Duncan, Safety, Quality and Allergens Manager and Katie Carter, Safety, Quality and Food Allergens Specialist

Food allergen cross-contact can occur at any stage of the food supply network, from ‘farm to fork’, and allergens cannot be removed or processed out of products once they are present. Therefore, effective food allergen management and accurate consumer information are essential for ensuring the safety of food for consumers with food hypersensitivity.

Food allergen risks are typically controlled through prerequisite programmes (PRPs) within ISO 22000 food safety management systems. These programmes establish the essential conditions and measures required to prevent and minimise allergen cross-contact.

Key PRPs for allergen management include:

• Supplier approval and assurance;
• Allergen segregation and zoning;
• Cleaning and sanitation;
• Personnel hygiene and training;
• Transport and storage controls;
• Rework management.

Below, we outline key stages in the food supply network where allergen cross-contact can occur, typical risks to consider, and how to control these allergen risks through robust PRPs that perform under pressure.

1. Agricultural

Food allergen contamination can be introduced even at the earliest stages of the food supply network. Cross-contact may occur through seed dispersal (where diverse crops are grown near each other), through the unintended mixing of seeds, where crop rotation is practiced, or due to remnants of crops persisting in fields.

Even where allergen cross-contact has not occurred, co-mingling of crops can still be problematic from an allergen perspective. Where it involves crop(s) that are closely related to an allergenic crop, cross-reactivity can occur in allergen testing, leading to false positive results.

These risks highlight the importance of PRPs such as raw material control and supplier assurance programmes.

Managing allergen risk at source requires clear supplier specifications, traceability and verification activities to ensure that incoming materials meet defined allergen requirements. If you need support with interpreting or investigating unexpected allergen results, reach out to our experts.

2. Harvesting, transport and storage

The risk of allergen cross-contamination increases during the busy harvesting periods when the use of shared harvesting equipment, transport vehicles and storage facilities intensifies. If cleaning is not adequately completed between uses, allergens can be transferred between batches.

As products move beyond the farm, there is further potential for cross-contact from co-transported goods with different allergen profiles. Careful consideration must therefore be given to load compatibility and transport hygiene.

EU legislation requires that equipment, conveyances and/or containers are cleaned after being used to transport allergenic foodstuffs and must be inspected for visible debris prior to reuse to mitigate the risk of food allergen cross-contact.

This highlights the importance of robust cleaning and sanitation programmes and effective segregation during transport, as expected within prerequisite programmes.

If you need support or guidance on cleaning and disinfection, reach out to our experts.

3. Processing

During processing, any allergen contamination that is already present may become more concentrated through initial operations such as milling, drying or freezing.

In terms of further contamination, within manufacturing environments there are multiple potential vectors of cross-contact, including personnel practices, the processing environment, shared equipment and utensils, and spillages of allergenic materials.

The safe management of these risks relies heavily on well-established PRPs, including:

• Personnel hygiene and training;
• Hygienic zoning and segregation;
• Equipment design and cleanability;
• Cleaning validation and verification.

Rework (material removed during processing and reintroduced later) requires particular attention and must be managed through defined procedures to ensure compatibility of allergen profiles and to prevent unintended introduction of allergens.

Effective allergen control in food processing depends on integrating allergen management into everyday operational practices, supported by monitoring and verification activities.

If you need support on allergen cross-contact precaution strategies, reach out to our experts.

4. Fraudulent and malicious contamination of raw materials

Even where internal controls are robust, risks may arise earlier in the supply network from fraudulent and malicious contamination of your raw materials. These represent more extreme scenarios but can have significant food safety implications, as described in PAS 96:2026.

Economically motivated adulteration (EMA) may involve the addition of undeclared substances to increase volume or reduce costs. While not always intended to create a food safety hazard, the use of allergenic materials as adulterants can pose serious risks to allergic consumers.

Malicious contamination, although less common, may involve the deliberate introduction of allergens not typically present in a product.

These risks are addressed through broader food safety and integrity programmes, including:

• Food fraud vulnerability assessment;
• Food defence planning;
• Supplier monitoring and approval systems.

Together, food fraud and food defence controls reinforce PRPs, enhancing the robustness and effectiveness of the overall food safety management system.

If you need support with protecting your business from EMA and malicious threats, reach out to our experts.

Managing allergen risks through food safety systems

Food business operators must implement effective food allergen management systems as part of their prerequisite programmes to mitigate or eliminate potential sources of cross-contact. Control measures should be validated, verified, routinely monitored and appropriately documented to demonstrate their effectiveness.

By embedding allergen controls within food safety management systems, businesses can achieve a structured and consistent approach to risk management, improving both compliance and consumer safety.

How we can help you control your allergen risks

Preventing allergen failures starts in your PRPs – so they need to consistently work under pressure to protect you. By working with our experts, you can strengthen your control of allergen risks across your food supply network.

We provide tailored, expert support across all aspects of food allergen management, helping food and drink businesses control risk with confidence – from supply chain to finished product. We offer a range of services, including training, testing, cleaning validation, hygienic design support, food safety management system development, gap analysis and allergen risk mapping, to help businesses build confidence in producing safe food.

By working with us, your business can benefit from:

• Specialist allergen and food safety expertise;
• Practical, proportionate, risk-based advice;
• Support aligned with regulatory expectations and best practice;
• Confidence in controls, labelling and decision making.

We can help

To find out more about managing allergen cross-contact risks across your supply network, get in touch

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