Why Allergen Controls Are a Top Priority Under FSMA

Food allergens are among the leading causes of FDA recalls, often due to undeclared allergens or cross-contact during processing. Because even trace amounts of allergens can lead to serious health consequences, the Food Safety Modernization Act (FSMA) requires facilities to implement Allergen Preventive Controls when a hazard requiring a preventive control is identified. According to 21 CFR §117.135(c)(2), the Preventive Controls Qualified Individual (PCQI) is responsible for overseeing the development of the food safety plan, which includes identifying allergen-related risks and ensuring that effective procedures are in place to prevent contamination and mislabeling.

When executed properly, allergen controls protect consumers with food allergies, maintain brand trust, and help facilities avoid costly recalls and legal action.

Step 1: Identify Allergen Hazards in Your Facility

Allergen control begins with a thorough understanding of where allergen risks exist in your facility. This includes both ingredients and operational practices.

Common allergen risks include:

• Use of any of the major nine allergens (e.g., milk, eggs, peanuts, tree nuts, fish, shellfish, soy, wheat, sesame)
• Shared equipment between allergen and non-allergen products
• Rework or reprocessing of allergen-containing materials
• Incorrect or outdated product labeling

Actionable Tip: Create an allergen matrix that maps out every allergen present by product, ingredient, and production line.

Step 2: Develop Written Allergen Control Procedures

Once risks are identified, the PCQI must ensure that the food safety plan includes preventive controls to prevent both cross-contact and labeling errors. These controls should be built into the facility’s Food Safety Plan and include:

Cross-Contact Controls

• Dedicated lines or production scheduling (e.g., allergen runs at end of shift)
• Proper sanitation between runs, validated for allergen removal
• Physical separation during storage and handling
• Color-coded utensils or equipment for allergen vs. non-allergen use

Labeling Controls

• Verification of label stock against product formulation
• Review procedures for label updates, reformulations, or co-packed items
• Pre- and post-labeling checks at packaging stations

Actionable Tip: Include allergen risk points in all SSOPs, especially those covering sanitation, changeovers, and packaging.

Step 3: Train Staff at All Levels

Allergen safety isn’t just the responsibility of the PCQI—it’s a team-wide commitment. Ensure:

• Sanitation staff understand allergen cleaning protocols and verification steps
• Production teams are trained on allergen handling, segregation, and scheduling
• Labeling personnel are educated on the importance of correct label application and checks

Actionable Tip: Reinforce allergen training with signage, visual reminders, and periodic testing during internal audits.

Step 4: Monitor and Verify Allergen Controls

Routine monitoring ensures allergen controls remain effective over time. Monitoring activities may include:

• Line clearance sign-offs between allergen and non-allergen runs
• Label verification logs before and during production
• Allergen swab testing of equipment and surfaces post-sanitation
• Visual inspection of storage and production areas for segregation compliance

Verification activities should confirm that controls are functioning and documented properly. This may involve:

• Reviewing sanitation records
• Reviewing label and packaging logs
• Conducting internal allergen audits

Actionable Tip: Use a “double-check” system for allergen labeling—requiring two separate verifications before product release.

Step 5: Respond Quickly to Deviations and Mislabeling Risks

When allergen control failures occur, the food safety plan designates the actions to be taken, and the responsibility for initiating immediate and structured corrective actions:

• Quarantine affected products
• Trace and assess scope of mislabeling or cross-contact
• Notify regulatory authorities if a recall may be required
• Conduct root cause analysis and retrain personnel as needed

Actionable Tip: Keep a templated recall protocol specifically for allergen-related events, including consumer notification language and regulator outreach procedures.

Avoiding Common Allergen Control Failures

• Inadequate sanitation validation → Swabbing must be specific to allergen proteins, not just general hygiene.
• Labeling assumptions → Never assume the correct label is loaded; verify each time.
• Untrained or rotating staff → Allergen controls break down when part-time or new hires aren’t fully trained.
• Undocumented exceptions → Any deviation must be logged and reviewed.

Actionable Tip: Audit allergen controls quarterly and review incident trends to close repeat gaps.

Protecting Consumers and Compliance Through Allergen Controls

Allergen control is more than a checkbox—it’s a public health responsibility. The PCQI ensures these programs are properly designed, documented in the food safety plan, monitored, and continuously improved to safeguard consumers with allergies and avoid regulatory penalties.

Registrar Corp offers PCQI training and allergen compliance support to help manufacturers implement effective allergen control systems and avoid costly recalls.