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Food safety6 min read

Allergen management: building an allergen matrix and preventing cross-contamination

Allergen management makes sure a customer with an allergy never unexpectedly consumes an allergen. That takes an overview of what is in your products, separation in your process and clear information. This is how you approach it, from matrix to training.

Where do allergens in the chain come from?

Allergens are not only in recipes. They enter via raw materials, via compound ingredients and processing aids, via rework, via shared equipment and via people. Someone with an allergy can react to very small amounts, so in practice a trace counts.

In the European Union fourteen allergens have been designated for which information is mandatory, such as cereals containing gluten, milk, egg, peanuts, nuts, soy, fish, crustaceans, celery, mustard and sesame. You can find the full and current list with the NVWA or the Dutch Nutrition Centre.

How do you build an allergen matrix?

An allergen matrix is a table with your products or recipes in the rows and the allergens in the columns. In each cell you note whether the allergen is present as an ingredient, may be present through cross-contamination or is not present. That shows at a glance what is in what.

Build the matrix from the specifications of your raw materials, not from memory, and appoint one owner who maintains it. A matrix that nobody manages is outdated within a few months and then more dangerous than no matrix, because people rely on it.

  • Collect all recipes and the current specifications of raw materials and processing aids
  • For compound ingredients, find out which allergens they contain
  • Enter the allergens present for each product in the matrix
  • Assess per production line whether cross-contamination is possible and note it separately
  • Have a second person check the matrix and give it a version number

Where does cross-contamination arise?

Cross-contamination occurs when an allergen unintentionally ends up in a product that should not contain it. The well-known routes are shared machines and tools, dust and splashes in the air, mixed storage, employees' hands and clothing, and rework that returns to the wrong product.

So walk through your process physically, from receipt to dispatch, and mark at each step where an allergen can jump across. Talk to the people on the line, because they know the places where things dust, leak or get reused. Record what you find, so that separation and cleaning are later based on real places.

Separating, scheduling and cleaning

Tackle cross-contamination in a fixed order: first separate, then schedule, then clean. Separation is the strongest, because what never meets does not need cleaning. Where separation is not possible, you schedule smartly and clean demonstrably. That keeps the number of risky moments as small as possible.

Visually clean is not the same as allergen-free. So support your cleaning method with a test for residues of the allergen or with laboratory analysis, and check periodically that the method still works. A method that works for one product does not necessarily work for a sticky or greasy one.

An example: a bakery makes a plain cookie and a hazelnut cookie on one line. If you bake the plain cookie first and the hazelnut cookie afterwards, you clean thoroughly after the last hazelnut run instead of after every changeover. You check that cleaning with a test before the line is used for the plain cookie again.

  • Separation: own line, room, tools or color coding for products with allergens
  • Scheduling: products without the allergen first, products with the most allergens last
  • Cleaning: a justified cleaning method between products, with a check afterwards
  • Storage and internal transport: closed, clearly labeled and separate where possible
  • Rework: only back into a product in which the allergen already belongs

What do you tell the customer?

For prepackaged products the allergens must be clearly shown on the label, for example by emphasizing them in the ingredient list. For non-prepackaged products, such as in catering and at the baker, you must be able to tell customers which allergens they contain. The rules differ per situation and change; check them with the NVWA and the Dutch Nutrition Centre.

Use a precautionary warning on the label only for a residual risk that you cannot exclude despite good measures. Never see it as a replacement for separation and cleaning. Agreements and guidelines exist for its use and these may change. So check regularly whether your way of working still meets them.

What changes with a new recipe or a different supplier?

The biggest risk lies in changes. A supplier replaces an ingredient, a new flavor goes over the same line, a recipe is slightly adjusted: any of these can add an allergen without anyone noticing. The product has then changed, while the matrix and the label still tell the old story.

Make allergens a fixed question in your change process and in purchasing. A change only goes ahead once the matrix, label and cleaning schedule have been updated. Ask your suppliers to pass on changes in allergen information immediately and agree who receives that within your organization.

  • Does the composition or specification of a raw material change?
  • Will the product run over a line that also processes other allergens?
  • Has the matrix been updated and checked by a second person?
  • Do the label, product information and menu match the new situation?
  • Has packaging with the old label been taken out of circulation?

Training: who needs to know what?

A matrix does not help if the employee on the line does not understand why they change gloves. Train everyone who works with product: what allergens are, why small amounts matter and which rules apply at your site. Give extra training to whoever handles recipes, labels or customer questions.

Record who was trained and when, and repeat it for new employees, temporary workers and after changes. Teach service staff that 'let me check that for you' is always better than guessing. A customer with an allergy relies on the answer, so a certain answer matters more than a fast one.

Common mistakes in allergen management

Allergen management rarely goes wrong through unwillingness, but through assumptions and forgotten handovers. Someone assumes an ingredient has been the same for years, or that yesterday's shift cleaned the line. Such assumptions are understandable, but they are exactly what an auditor, an inspector or an allergic customer brings to light. This is what you see most often:

  • A matrix made once and never updated afterwards
  • Looking only at ingredients and not at shared equipment, rework and storage
  • Cleaning without demonstrating that the allergen is really gone
  • Using a precautionary warning instead of control
  • Not passing on supplier changes to production and labeling

How BrydgeOne supports this

The Allergen management module helps you control the allergen matrix and cross-contamination. If you also use HACCP & hazard analysis for your food safety plan, Supplier management to evaluate and monitor suppliers and Training for e-learning with tests, you manage the parts of this guide in one place.

© 2026 BrydgeOne. General information, not legal or other professional advice. No rights can be derived from this article.

Frequently asked questions

Frequently asked questions

Is an allergen matrix mandatory in catering?

The matrix as a document is not mandatory as such. However, you must be able to tell customers which allergens are in a dish. A matrix or recipe overview is the most reliable way to do that, especially with changing menus. Check the current rules for non-prepackaged food.

How do I know which allergens my supplier delivers?

Ask for a current specification with allergen information, including a statement on cross-contamination at the supplier. Have it renewed periodically and confirmed at every change. Also include it in your supplier evaluation, so you know who informs reliably and who does not.

What do you do if a product contains an allergen that is not on the label?

Treat it as a food safety issue: stop delivery, hold the batch and start your recall procedure if product has already reached customers. Inform the authority and customers according to the applicable rules. Then find the cause and record a corrective and preventive action.

See how BrydgeOne supports this

You only pay for the modules you switch on, from € 49 per month. In a demo we show how it works with your own processes.