Effective Allergen Management in Food Production

Allergens are one of the most common and serious food safety risks in modern food production. They are also the leading cause of food recalls in the United States.

Unlike microbial hazards, allergens cannot be eliminated through cooking, sanitation, or processing steps alone. Once an allergen is unintentionally introduced into a product, there is no corrective step that can make that product safe for an allergic consumer. The only true control is prevention.

For food producers, allergen management is not simply a compliance exercise. It is a core responsibility tied directly to consumer safety, brand trust, and business continuity. For small and mid-sized operations, a single allergen failure can trigger recalls, regulatory action, and long-term reputational harm.

It is also one of the most misunderstood areas of food safety.

Effective allergen control is not achieved through labels alone. It is a system that begins with ingredient sourcing and extends through storage, production, sanitation, packaging, verification, and ongoing review.

Many allergen failures stem from informal practices that developed over time and were not documented, trained, or revisited as operations changed. Allergen management is not about starting from scratch. It is about making existing practices intentional, visible, and repeatable.

Why Allergen Control Is So Challenging

Allergens move easily through food facilities and are often invisible once introduced.

Common challenges include:

• Shared equipment used for allergen and non-allergen products

• Airborne powders such as milk, wheat, or soy proteins

• Rework or trim added back into multiple formulations

• Supplier changes that alter allergen status without visual cues

• Human error during staging, changeovers, or labeling

Unlike pathogens, there is no kill step for allergens. A single missed control can result in misbranding or a recall, even when all other food safety parameters are met.

Start With a Clear Allergen Hazard Analysis

Effective allergen management begins in the hazard analysis. This is where many programs fail, not because allergens are ignored, but because they are treated informally.

In the United States, the major food allergens are milk, eggs, fish, crustacean shellfish, tree nuts, peanuts, wheat, soybeans, and sesame.

A strong allergen hazard analysis should:

• Identify all major allergens present in ingredients, processing aids, and rework

• Evaluate where cross-contact could occur during storage, processing, or packaging

• Address both intentional allergens and unintended exposure

• Clearly define how allergens are controlled through formulation, segregation, sanitation, scheduling, or labeling

If allergens are present in a facility, they must be addressed as a chemical hazard with documented controls. General statements such as “we clean carefully” are not controls unless they are supported by written procedures, records, and verification activities appropriate to the operation.

FSIS inspection context:

In USDA FSIS-inspected establishments, allergen control is evaluated through the hazard analysis and supporting prerequisite programs, with particular emphasis on labeling accuracy. Allergen related failures are most often cited as misbranding, even when the underlying process controls are otherwise sound. This makes clear documentation, recordkeeping, and linkage between formulation, labels, and production practices especially important in federally inspected operations.

Ingredient Control and Supplier Management

Allergen management starts before ingredients arrive at the facility.

Effective programs include:

• Maintaining current ingredient specifications and allergen statements from suppliers

• Verifying allergen status whenever suppliers, formulations, or processing aids change

• Reviewing incoming ingredients against an approved ingredient list

• Clearly labeling and segregating allergen-containing ingredients upon receipt

Supplier documentation must be reviewed routinely. Many allergen recalls originate from supplier changes that were not communicated, reviewed, or documented internally.

Segregation, Storage, and Production Scheduling

Physical separation is one of the most effective allergen controls available, but it is also one of the most misunderstood.

Regulators do not require a single correct storage layout. They require that cross-contact is prevented and that the system in place is understood, followed, and documented.

Separation does not always mean a separate room or a perfect layout. It means preventing cross-contact in real spaces with real constraints.

Where feasible, operations should:

• Store allergen-containing ingredients in clearly designated and labeled areas

• Use dedicated utensils, containers, or tools for allergen products

• Apply visual systems, such as color coding, to reinforce separation

When full segregation is not possible, production sequencing becomes critical. Running non-allergen products first, followed by allergen-containing products, reduces cross-contact risk and limits the scope of sanitation required between runs.

Dry Storage and Cold Storage

Same Risk, Different Failure Modes

Allergens behave the same in dry storage, refrigerated storage, and frozen storage. Cold temperatures do not reduce allergen risk. They only change how cross-contact occurs.

In dry storage, allergen failures most often result from airborne powders, gravity-driven spills, overstacking, and shared handling tools. In cold storage, failures more commonly involve condensation, leaking or thawing product, crowding, and temporary staging during production or delivery. The controls do not change, but the points of attention do.

Dry storage failures usually come from dust and gravity. Cold storage failures usually come from moisture and crowding.

Because storage and staging are such common sources of allergen failures, practical storage rules are addressed in our one-page Allergen Storage Field Guide designed for posting and day-to-day use across USDA FSIS, FDA, retail, restaurant, deli, butcher shop, and shared kitchen environments.

DOWNLOAD ALLERGEN GUIDES

Allergen Storage Field Guide (PDF for posting and staff training)

Cleaning and Sanitation Controls

Sanitation is often assumed to control allergens, but not all cleaning methods effectively remove allergenic residues.

An allergen-focused sanitation program should include:

• Written procedures specific to allergen removal, not only general cleaning

• Defined disassembly steps for shared equipment

• Visual inspection combined with appropriate verification methods

• Records showing that cleaning is performed as written

If sanitation is used as a critical allergen control, there must be evidence appropriate to the operation that the method works under actual production conditions. The level of verification should match the risk, the product, and the process.

In FSIS-inspected facilities, allergen-related sanitation controls are often evaluated during pre-operational inspection and at changeovers, making consistency between written procedures, observed practices, and records essential.

Labeling Accuracy Is a Critical Control

Labeling is the final safeguard for allergic consumers and one of the most common points of failure.

Common labeling errors include:

• Using outdated labels after formulation changes

• Applying the wrong label during packaging runs

• Failing to update allergen statements when ingredients change

• Relying on precautionary statements instead of real controls

Labeling failures are treated as misbranding violations and frequently result in recalls even when the product itself is otherwise safe. Best practices include label verification at startup, during production, and at every changeover. Finished product labels must match the actual formulation every time.

Training and Accountability

Allergen control systems only function when employees understand why they matter.

Training should cover:

• Which allergens are present in the facility

• How cross-contact occurs

• Why small mistakes can have serious consequences

• Each employee’s role in preventing allergen exposure

Training must be documented and refreshed whenever products, ingredients, equipment, or processes change. Allergen management is not optional or theoretical. It is a daily responsibility.

Verification and Continuous Review

Allergen programs are not static. They require ongoing oversight.

Effective verification includes:

• Internal reviews focused on allergen controls

• Routine review of sanitation and labeling records

• Monitoring supplier and formulation changes

• Investigating near misses and corrective actions

Programs must evolve as operations grow, equipment changes, or new products are introduced.

The Final Word

Effective allergen management is built on prevention, documentation, and discipline. It requires coordination across purchasing, production, sanitation, labeling, and training.

For producers, strong allergen controls protect consumers, preserve trust, and reduce recall and regulatory risk. For regulators, they demonstrate that hazards are understood and controlled, not assumed away.

These principles only work when they are visible on the floor. Storage, staging, labeling, and training decisions made every day are where allergen control succeeds or fails. Clear systems, reinforced through consistent practice and documentation, are what keep prevention intact over time.

AgriForaging Compliance Services works with food businesses to design allergen management programs that reflect real facilities and real workflows while meeting regulatory expectations. If your products, suppliers, equipment, or processes have changed, it is time to reassess how allergens are identified, controlled, stored, and verified across your operation.