Food Allergen Testing: How It Supports Quality Assurance Programs

With approximately 33 million Americans affected by food allergies, food manufacturers face consumer safety risks from undeclared allergens and cross-contact. Undeclared allergens were also the most common reason for U.S. food recalls in 2025, accounting for 38.8% of the 320 recalls issued by the FDA and USDA.

Food allergen testing helps your quality assurance (QA) team detect potential contamination and evaluate existing allergen controls. Through laboratory analysis, you can assess cleaning effectiveness, monitor production risks, and make informed quality decisions.

What Is Food Allergen Testing?

Food allergen testing detects specific allergenic proteins or related markers in food products, ingredients, and environmental samples. It helps your QA team investigate potential allergen presence and evaluate existing controls throughout production.

Testing ingredients, finished products, equipment surfaces, and rinse water helps your team investigate potential cross-contact. These findings also support assessments of established allergen controls.

Why Is Food Allergen Testing Important for Quality Assurance?

Your QA program relies on established procedures to manage allergen risks throughout production. Laboratory testing provides analytical evidence that helps evaluate whether these procedures are working as intended.

That means nearly four in ten recalls involved an allergen that was missing from the label, which is why your QA program needs evidence that its allergen controls are working.

Consider a facility producing both dairy-containing and dairy-free products. Shared equipment can create opportunities for milk proteins to transfer between production runs.

Even after cleaning, allergen residues might remain on processing surfaces. Targeted testing can help determine whether those residues are detectable in collected samples.

Testing also supports your QA program in several ways:

•  Helps evaluate established allergen control measures.
• Identifies potential cross-contact concerns requiring investigation.
• Provides documented results for routine QA monitoring.
• Supports investigations and follow-up corrective actions.

Your team can compare testing results with production records and ingredient specifications. Recurring findings can also reveal areas requiring closer evaluation.

How Allergen Testing Supports QA Programs

Allergen risks can arise at different stages of food production. Your testing activities should reflect the ingredients handled, equipment used, and potential sources of cross-contact.

Allergen testing can support your team at several stages of food production.

Assessing Raw Materials and Ingredients

Incoming food ingredients can introduce unintended allergens, especially when suppliers process multiple allergenic materials.

For example, a supplier might use shared equipment for peanut-containing ingredients and products formulated without peanuts. Insufficient cleaning may leave allergen residues that could transfer between these materials.

Targeted testing can help investigate the presence of suspected allergens in incoming ingredients. Your team can compare laboratory findings with supplier documentation and established ingredient specifications.

Testing also supports investigations involving ingredients selected for new food product formulations. Your product development team can use analytical findings when reviewing potential allergen concerns associated with ingredient changes.

Verifying Cleaning Effectiveness

Shared food processing equipment requires appropriate cleaning procedures to control allergen residues.

Consider a bakery that switches between peanut butter cookies and cookies made without peanuts. Residues left on mixers or conveyors could introduce unintended allergens into subsequent batches.

Allergen-specific surface swabs can help detect targeted proteins following equipment cleaning. Rinse water testing can also support verification when suitable for the cleaning procedure.

Cleaning validation and verification serve different purposes:

• Cleaning validation establishes whether a defined cleaning procedure can achieve its intended result under specified conditions.
• Cleaning verification checks whether the established cleaning procedure continues performing as intended during routine operations.

Both activities require suitable testing methods and documented procedures. Results can help your team investigate cleaning concerns and evaluate existing controls.

Monitoring Allergen Cross-Contact During Production

Allergen cross-contact can occur through shared food processing equipment, ingredient handling, or contact between different products.

Targeted testing helps investigate potential allergen transfers at selected production stages. Sampling locations should reflect your facility’s identified risks and established monitoring procedures.

For example, the unexpected detection of an allergen near shared equipment could prompt a review of cleaning records. Your team might also examine production schedules or ingredient handling practices.

These findings can help identify weaknesses in existing controls. Addressing those weaknesses can reduce the likelihood of recurring cross-contact concerns.

However, testing detects potential problems rather than physically preventing allergen transfer. Prevention still depends on appropriate production controls and consistent operating procedures.

Evaluating Finished Food Products

Finished product testing provides additional information when investigating the potential presence of unintended allergens in food products.

Your team might request laboratory analysis following a suspected cross-contact incident or unexpected ingredient change. Testing can help determine whether targeted allergens are detectable in submitted samples.

These findings can support investigations alongside production records and other available evidence.

Supporting Accurate Allergen Labeling

Accurate food allergen labeling helps consumers identify ingredients that could trigger allergic reactions.

For food manufacturers, labeling accuracy depends on ingredient specifications, formulation records, and appropriate packaging controls. Laboratory testing provides additional evidence when investigating potential undeclared allergens in finished food products.

A study of FDA recalls from fiscal years 2013 to 2019 found that labeling-associated errors accounted for 71.1% of major food allergen recalls with known root causes.

For example, an unexpected detection of milk protein in a product could prompt your QA team to investigate potential cross-contact. Testing results can also support further review of ingredient specifications and labeling records.

Supporting Corrective Actions and QA Documentation

Unexpected allergen results can indicate potential weaknesses in existing food production controls.

Your team can investigate the affected process and review relevant production records. Findings might reveal cleaning concerns, ingredient handling issues, or other sources of cross-contact.

Depending on the investigation, corrective actions could involve revised procedures or additional verification activities.

Documented results also help your team track recurring concerns. For example, repeated allergen detection at one sampling location could suggest an unresolved cleaning issue.

Reviewing previous findings can help identify patterns requiring further investigation. These records support ongoing assessments of your allergen management procedures.

Common Food Allergen Testing Methods

Allergen testing for food manufacturers uses different methods to detect specific substances or ingredient-related markers. The appropriate method depends on your target allergen, sample characteristics, and testing objectives.

Common types of food allergy testing include:

• Enzyme-linked immunosorbent assay (ELISA): Detects specific allergenic proteins through antibody-based reactions. Depending on the test, it can measure allergen concentrations in ingredients and finished food products.
• Lateral flow tests: Detect specific allergens in food, on equipment surfaces, or in rinse water using test strips. They provide rapid results indicating whether the targeted allergen is detected at a specified threshold.
• Polymerase chain reaction (PCR): Detects DNA associated with specific allergenic ingredients, such as peanuts or soybeans. It helps identify ingredient-related material in food samples but does not directly measure allergenic proteins.
• Mass spectrometry: Identifies allergen-related proteins or peptides by measuring their molecular characteristics. It supports detailed allergen analysis in food samples, particularly when specialized identification is needed.

Analytical chemistry support services can help manufacturers select appropriate testing methods for their products and quality requirements.

What Should Food Manufacturers Consider When Planning Allergen Testing?

Your allergen testing plan should align with your food safety plan and identified production risks.

Key considerations include:

• Identify target allergens based on your food ingredients and production processes.
• Select sample types and locations according to potential cross-contact risks.
• Establish testing frequency based on food production activities and existing controls.
• Choose analytical methods appropriate to the target allergen and the food sample characteristics.
• Define procedures for documenting results and investigating unexpected findings.

Review your testing plan when ingredients, equipment, or production processes change. New changes may introduce different allergen risks.

Frequently Asked Questions

What Are the Common Food Allergens?

Nine major food allergens, commonly known as the Big 9, are recognized by the U.S. Food and Drug Administration (FDA):

• Milk
• Eggs
• Fish
• Crustacean shellfish
• Tree nuts
• Peanuts
• Wheat
• Soybeans
• Sesame

Which Food Contains a Major Allergen Recognized by the FDA?

Common examples include peanut butter (peanuts), cheese (milk), bread (wheat), and mayonnaise (eggs). Manufacturers should review product formulations and ingredient specifications, as allergens vary across food products.

Are Food Manufacturers Required to Declare Allergens on Product Labels?

Yes. The U.S. Food and Drug Administration (FDA) requires most packaged foods to declare any of the nine major allergens used as ingredients. Manufacturers must identify these allergens in the ingredient list or a separate “Contains” statement.

Which Is a Common Food Allergen in Food Manufacturing?

Milk is a common food allergen found in dairy products, baked goods, sauces, and processed foods. Other common allergens include eggs, peanuts, wheat, soybeans, and sesame, depending on the ingredients used.

What Should Food Manufacturers Look for in Food Allergen Testing Laboratories?

Look for a laboratory that offers testing methods suited to your target allergens and food products. Consider its analytical capabilities, detection limits, turnaround times, and reporting procedures.

Strengthening Quality Assurance Through Food Allergen Testing

Your allergen management program depends on established controls and evidence that supports their ongoing evaluation.

Food allergen testing provides analytical information to assess cleaning effectiveness and investigate potential cross-contact. It also supports ingredient assessments, labeling investigations, and documented QA reviews.

Matrix Sciences provides food safety and quality testing services to support your organization’s analytical needs. These solutions provide documented results to help evaluate existing allergen controls.

Contact Matrix Sciences to discuss your food safety testing needs.