How Food Facility Design Can Improve Allergen Control and Prevent Cross-Contact

As allergen expectations shift toward stronger prevention, validation, and risk-based controls, food producers should consider how facility design can prepare them for what comes next.

Food facility owners planning a renovation, expansion, new production line, or greenfield facility should evaluate whether their layouts support allergen segregation, hygienic design, sanitation, material flow, dust control, testing, and future production needs. This article identifies the facility-design decisions that can help reduce allergen cross-contact risk while improving operational efficiency and adaptability.

More than 33 million Americans live with food allergies, according to Food Allergy Research & Education. This reality continues to make allergen control a public health and regulatory priority, and a major business concern for producers, processors, and brand owners. For food producers, the challenge goes beyond listing major allergens on a label. Processors also bear responsibility for how ingredients move through a facility, how products are segregated, how sanitation is planned and executed, and how packaging lines are arranged.

Regulatory developments add another layer to long-term facility planning. FDA’s January 2025 food allergen labeling guidance, Guidance for Industry: Questions and Answers Regarding Food Allergen Labeling (Edition 5), adds sesame as the ninth major allergen and clarifies the declaration of several other ingredients. Separate FDA discussions explore possible applications for allergen thresholds, including advisory labeling, compliance decisions, and cross-contact controls. International Codex guidance and private-sector audit standards provide additional direction for managing allergens across supplier and production operations.

So how can food and beverage manufacturers approach, and improve, allergen control in such a dynamic regulatory environment? Start at the beginning — with smart facility design.

Beyond the Label: How Food Facility Design Supports Allergen Control

Allergen control starts with a product, a process, and a risk assessment. Once those decisions are made, the facility must support them. A plant layout influences how ingredients are received, stored, staged, sampled, tested, transferred, processed, packaged, and shipped. The layout also affects employee movement, equipment access, sanitation sequencing, air movement, dust control, and the ability to separate incompatible products or processes.

Allergen strategy should therefore be integrated into food manufacturing facility planning, design, and engineering from the outset. Design discussions should address not only current requirements but also how readily the operation can adapt as standards, customer expectations, third-party audit requirements, and testing practices evolve.

While solid design is simpler with greenfield projects, facility renovations can be more complex due to the often-haphazard nature of previous efforts or quick-fix attempts to squeeze more out of an outdated operation. Streamlining an existing facility layout for food allergen safety usually requires significant reorganization.

How to Design a Food Facility Around Production-Specific Allergen Risks

Every production environment is different. A bakery, beverage facility, ready-to-eat food operation, frozen-food plant or dry-mix operation carries its own allergen risks and control needs. Product category, ingredient profile, cleaning methods, process flow, and packaging format all influence how the facility should be planned. Thus, how allergen control is addressed will vary based upon the type of products and the type of facility.

The more products a facility produces, the more challenging allergen control becomes. Production schedules and shifts must be planned to provide appropriate separation. If the facility was not originally designed for that separation, operations have to adapt—often creating inefficiencies. Streamlining the layout may require segmenting the operation or reworking how products, people, and materials move through the plant.

Through an understanding of both the practical production needs and the challenges food allergens introduce, Foth | Food Plant Engineering helps manufacturers think through space arrangement decisions and segment operations so producers may not have to rely solely on scheduling or workarounds. It is not unusual for operations managers to develop tunnel vision after looking at and working in the same facility for so long. A fresh set of eyes and decades of experience working with food producers can yield new or creative ideas that lead to a more efficient layout designed to reduce allergen cross-contact risk.

Allergen Control in Receiving, Storage, Production and Packaging

Though every facility is unique, receiving and storage are particular areas that warrant attention in most operations. If incoming ingredients must be sampled or tested, the design should provide appropriate staging or holding areas so materials can be controlled before release into production. Allergen-containing ingredients may need designated storage, clear separation or other controls based on the facility’s risk assessment. Finished goods may also require hold areas when release depends on testing, documentation or quality review. Again, these are not generic square-footage questions; they are operational decisions that should be reflected in the layout.

Production flow deserves the same attention. Shared equipment, product changeovers, dry versus wet sanitation, dust control, employee traffic and packaging-line adjacency can all influence cross-contact risk. In some facilities, separation may mean dedicated rooms. In others, it may involve sequencing, controlled traffic patterns, barriers, ventilation considerations or updated sanitation design. The right approach depends on the products being made and the risks that must be managed. When it comes to allergen control in food production, a one-size-fits-all solution is inappropriate.

Designing Food Facilities for Future Allergen Requirements

Food allergen requirements continue to evolve. Today’s framework emphasizes accurate ingredient disclosure, truthful labeling, current good manufacturing practices, and preventive controls. Future policy may place greater weight on risk-based tools such as allergen thresholds, documented sanitation effectiveness, supplier records, and evidence supporting advisory language such as “may contain.” The FDA has not established or endorsed allergen threshold levels, but recent public meeting activity (Virtual Public Meeting and Listening Session on Food Allergen Thresholds and Their Potential Applications – 02/18/2026 | FDA confirms that the agency continues to examine the issue.

For facility owners, this is important because buildings, utilities, and process layouts often outlast the regulatory guidance that informed them. A design that barely satisfies today’s needs may become difficult or expensive to adapt later. A forward-looking facility aligns the physical plant with the realities of ingredient control, cross-contact prevention, sanitation, testing, storage, packaging, and documentation (record keeping). It also provides flexibility through space allowance for future testing or holding, a layout that supports ingredient and product segregation, cleanable materials suited to the sanitation method used or planned, utilities that can serve current and future equipment, and production flows that can accommodate third-party audits and evolving consumer expectations.

Food producers do not need to predict every future requirement. Yet it is wise to create a facility that helps manage risk thoughtfully and can adapt as science, regulation, and consumer expectations change.  By protecting the consumer, the manufacturer protects the trust consumers place in them and their products.

When to Engage a Food Facility Design and Construction Partner

Foth | Food Plant Engineering’s design and construction professionals do not replace a company’s quality assurance, regulatory, or food safety teams. Those teams define the product risks, label requirements, validation needs, and operating procedures. But an experienced food facility design partner can translate those requirements into practical space, flow, material, utility and construction decisions.

A specialized design team asks the right questions early: What ingredients create allergen risk? Where could cross-contact occur? How will products be scheduled? What sanitation methods will be used? Will materials or finished goods need to be sampled, tested or held? How should people, packaging, ingredients and waste move through the facility?

Those questions help producers avoid treating allergen control as an afterthought. Early design discussions also support investment decisions that protect both food safety and operational efficiency.

In a renovation, expansion, relocation, new production line, or greenfield facility, the selected project delivery approach can influence how effectively food safety requirements are incorporated into design and construction.

Food Facility Allergen Control Design Checklist

• Are allergen-containing ingredients physically separated in receiving and storage?
• Are staging and holding areas available for sampled or unreleased materials?
• Can people, ingredients, packaging and waste move without creating cross-contact paths?
• Is shared equipment accessible and designed for effective cleaning?
• Does the ventilation strategy account for airborne dust?
• Can production lines be isolated without relying solely on scheduling?
• Is there room for future testing, holding or packaging requirements?
• Do layouts support SQF, BRCGS, FSSC 22000 or customer audit expectations?
• Can the facility accommodate new products or allergens without major reconstruction?

Is your facility prepared for changing allergen risks?

Foth | Food Plant Engineering can assess your existing layout, identify design constraints, evaluate the appropriate project delivery method, and help develop practical options for a renovation, expansion, relocation, new line, or greenfield facility.