Why Allergens Demand Unified Oversight

Allergens remain one of the most common causes of recalls in the U.S. food supply—and one of the most heavily scrutinized areas during both FDA inspections and GFSI audits. For facilities governed by FSMA’s Preventive Controls for Human Food and pursuing or maintaining SQF certification, allergen management is not a standalone program—it’s a system-wide responsibility.

That responsibility often falls to the Preventive Controls Qualified Individual (PCQI), who must design, validate, and oversee allergen controls that satisfy the regulatory requirements of FSMA and the operational rigor of SQF.

This article breaks down how the PCQI integrates allergen management practices across these two systems to build robust, compliant, and audit-ready programs.

1. Comparing FSMA and SQF Allergen Requirements

FSMA and SQF both emphasize allergen control, but their requirements differ in nuance and documentation.

FSMA Preventive Controls Rule requires:

• Identification of undeclared allergen risks as part of hazard analysis
• Implementation of Allergen Preventive Controls (APCs)
• Written procedures for label review, equipment cleaning, and ingredient control
• Verification and validation of these procedures

SQF Code, Edition 9 requires:

• Risk-based allergen management plans covering handling, storage, sanitation, and labeling
• Dedicated or segregated storage for allergens
• Clear identification of allergenic ingredients and cross-contact zones
• Regular training and documented verification of allergen procedures

Key Insight: FSMA focuses on preventing undeclared allergens through defined controls. SQF adds operational expectations for infrastructure, training, and environmental control.

2. Building a Unified Allergen Control Strategy

The PCQI’s role is to bridge FSMA’s regulatory obligations with SQF’s procedural and documentation requirements.

A unified approach involves:

• Conducting an allergen risk assessment as part of the facility’s hazard analysis
• Designing allergen preventive controls that double as SQF-compliant SOPs
• Establishing cleaning validation procedures that meet both FSMA and GFSI audit standards
• Including allergen label verification in the Food Safety Plan and daily QA routines
• Incorporating allergen changeover procedures into production scheduling and traceability systems

Actionable Tip: Develop an Allergen Control Map that shows where allergens exist in your process, how cross-contact is prevented, and how each control satisfies both FSMA and SQF criteria.

3. Documentation and Verification That Satisfy Both FSMA & SQF

One of the PCQI’s primary responsibilities is documentation. Allergen records must be clear, current, and defensible under scrutiny.

Essential documents include:

• Allergen hazard analysis with rationale for controls
• Written Allergen Preventive Controls (e.g., cleaning SOPs, changeover procedures)
• Verification records (swabbing results, label checks, staff training logs)
• SQF audit-ready summaries that link allergen management back to site risk assessments
• Evidence of ongoing reassessment and continuous improvement initiatives

Pro Tip: Conduct quarterly reviews of allergen-related deviations and verification logs to spot patterns or training gaps.

4. Cross-Training for Allergen Awareness and Compliance

Both FSMA and SQF emphasize the human element in allergen control. The PCQI plays a key role in driving cross-functional awareness and accountability.

Effective PCQIs:

• Train line operators and sanitation teams on the risks and responsibilities of allergen handling
• Involve QA, R&D, and procurement in allergen reviews and label control
• Lead mock recalls or internal audits with an allergen-specific lens
• Ensure refresher training is documented and aligned with role-specific responsibilities

Registrar Corp offers PCQI and allergen management training to help food safety professionals align their programs with current FSMA and SQF standards.

Raising the Bar on Allergen Control Through Integrated Oversight

As allergen risk continues to top the list of FDA enforcement priorities and GFSI non-conformances, facilities can no longer afford fragmented or siloed programs.

A PCQI who understands how FSMA and SQF intersect creates a cohesive allergen strategy that prevents errors, passes audits, and protects both consumers and brand reputation.

Facilities with fully integrated allergen programs are better positioned to respond to customer inquiries, supplier questionnaires, and third-party audits—demonstrating leadership and control in one of the industry’s most scrutinized risk areas.