Allergen-Free Co-Packing: How to Scale Clean-Label Products Without Cross-Contamination

The clean-label movement has fundamentally changed consumer expectations in the food industry. For brands serving consumers with food allergies or sensitivities, allergen-free manufacturing is not just a nice-to-have feature but a non-negotiable requirement that can make or break your ability to scale.

Finding a co-packer that can deliver true allergen-free production is harder than most brands expect. Many facilities claim allergen controls but still process multiple allergens in the same space, relying on cleaning protocols to manage cross-contamination risks. For brands committed to serving the food allergy community, that approach introduces liability and undermines consumer trust.

At Flatiron Food Factory, we built our facility specifically to eliminate cross-contamination concerns. Our Loveland, Colorado location is gluten-free and completely free from the top nine allergens. We don't process any of these allergens anywhere in our facility, which means brands can scale production without constant worry about trace contamination.

Why Shared Facilities Create Unavoidable Risk

Most co-packers operate shared facilities that process multiple product lines containing different allergens. They manage cross-contamination through scheduling, cleaning procedures, and allergen testing. While these practices reduce risk, they cannot eliminate it entirely. Equipment with complex geometries like freeze dryers, grinders, and mixers can harbor allergen residues even after thorough cleaning. Airborne particulates from one production run can settle on surfaces used in subsequent runs. Shared receiving docks and storage areas create additional contamination pathways.

For brands targeting consumers with severe food allergies, even trace amounts of allergens can trigger reactions. Parents shopping for their allergic children scrutinize labels and research manufacturing practices. They know that "processed in a facility that also processes" disclaimers signal real contamination risks, and they avoid those products accordingly. The result is that brands using shared allergen facilities either need to include these disclaimers, which limits their addressable market, or they operate without disclaimers while accepting liability exposure that grows with every unit sold.

Beyond the immediate safety concerns, shared facilities create operational headaches that slow production and increase costs. Changeover procedures between allergen-containing runs and allergen-free runs require extensive equipment teardown, cleaning validation, and testing. Production schedules become rigid because allergen-free runs must be carefully sequenced to minimize contamination risk. Lead times stretch out because the co-packer needs to batch similar products together. For growing brands that need production flexibility and quick turnarounds, these constraints become increasingly problematic.

What True Allergen-Free Manufacturing Looks Like

A genuinely allergen-free facility is designed from the ground up to eliminate cross-contamination pathways rather than just manage them. This starts with the ingredient sourcing and receiving process. Every ingredient that enters the facility must be verified allergen-free through supplier documentation and certificates of analysis. Receiving areas need protocols to prevent contaminated materials from ever entering the production environment. This seems basic, but it requires disciplined supplier management and receiving procedures that many facilities skip.

The production environment itself needs to be dedicated exclusively to allergen-free processing. Equipment, tools, utensils, cleaning supplies, and even the packaging materials need to stay within the allergen-free facility. Staff working in allergen-free production should not rotate between allergen-containing areas and allergen-free areas within the same shift. Air handling systems should maintain positive pressure and adequate filtration to prevent airborne contamination. These facility design choices create a controlled environment where cross-contamination risks are eliminated rather than merely reduced.

Documentation and traceability systems need to support allergen-free claims throughout the production process. This means maintaining detailed records of ingredient sourcing, production batch records, cleaning procedures, and finished product testing. For brands selling into retail channels or institutional accounts, this documentation provides the verification that buyers need to feel confident in your allergen-free claims. Without robust traceability, your allergen-free positioning becomes difficult to defend if questions arise.

Scaling Production Without Compromising Safety

Maintaining safety standards while scaling is one of the biggest challenges allergen-free brands face. Small-batch production in a startup facility is relatively easy to control, but as order volumes grow and you transition to a co-packer, options narrow considerably. Most large co-packers operate multi-allergen facilities to maximize equipment utilization, making dedicated allergen-free facilities with adequate capacity difficult to find.

Flexible minimum order quantities matter significantly for growing brands. High minimum runs force you to tie up cash in excess inventory or limit your product line. We work with brands at different stages, offering minimums from 500 to 100,000 pounds depending on the product. Production lead times also become critical as you scale. Facilities prioritizing allergen-free production exclusively can often respond faster because they do not need to schedule around allergen changeovers.

Due Diligence Questions for Evaluating Co-Packers

When vetting potential allergen-free co-packing partners, your questions will reveal whether a facility truly prioritizes allergen-free manufacturing. Start by asking if they process any of the top allergens anywhere on site. If they process allergens in separate rooms within the same building, ask about shared air handling systems, personnel, and ingredient receiving areas. These shared elements create contamination pathways that cleaning cannot fully eliminate.

Ask about ingredient verification and how they ensure every ingredient is actually allergen-free. Request sample certificates of analysis and supplier qualification procedures. A robust allergen-free program requires documentation at every step, not just final product testing. Request information about cleaning procedures and testing protocols for finished products. Regular environmental monitoring demonstrates ongoing commitment rather than one-time certification.

Why USDA Oversight Adds Another Layer of Assurance

USDA inspection provides quality assurance that extends beyond meat safety. Facilities operating under USDA oversight maintain rigorous sanitation standards, documented procedures, and regular inspections. These standards create operational discipline that benefits all products processed in the facility.

For allergen-free brands, USDA oversight means the facility already operates with detailed documentation, traceability protocols, and quality control as baseline requirements. Federal inspectors reviewing production regularly create accountability that reinforces food safety practices. The combination of USDA inspection and dedicated allergen-free facility design addresses both safety requirements and documentation needs that retailers and institutional buyers expect.

Making the Switch to Allergen-Free Manufacturing

Transitioning to a dedicated allergen-free facility requires planning but delivers immediate benefits in reduced liability and improved market positioning. Start by qualifying ingredient suppliers to ensure they can provide allergen-free materials with appropriate documentation. Product formulation sometimes needs adjustment when moving to allergen-free manufacturing, particularly if you have been using ingredients with hidden allergens. Working with a co-packer experienced in allergen-free formulation helps identify necessary changes while maintaining the quality your customers expect.

Once production begins, you can update packaging to reflect the allergen-free manufacturing environment. This messaging resonates strongly with consumers searching for truly safe options. Many brands see immediate sales increases after making this switch because they can finally market to the food allergy community with confidence.

At Flatiron Food Factory, we have been working with natural food brands and clean-label manufacturers since 2014. Our facility in Loveland, Colorado combines USDA inspection with complete allergen-free processing, giving brands the quality assurance and contamination controls they need to serve the food allergy market effectively. We offer freeze-drying services for proteins, bulk ingredients, and finished products, with flexible production volumes that support brands at every stage of growth.

If you are ready to explore allergen-free co-packing for your brand, reach out to discuss your specific needs and production requirements. We work with companies launching new products and established brands looking to improve their manufacturing processes. Our team can walk you through our facility capabilities and help you determine whether allergen-free freeze-drying aligns with your product development goals.

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