HACCP Allergen Control Program Guide: 5 Key Goals and Free Template

A HACCP allergen control program is important to maintain food safety.

The FDA has identified that allergic reactions to foods can range from simple itching to severe cases where the body develops respiratory problems called anaphylaxis.

As such, food authorities have established allergy policy regarding allergens such as their declaration in the food packaging. As a food manufacturer, you have to create a safe food processing course for your consumers. A step toward this goal is having an HACCP Allergen Control Program.

An allergen program is one of the crucial prerequisite programs of a HACCP plan as it involves critical control points. In America alone, about 50 million people are allergic to some types of foods. Studies have shown that at least 1 in 13 children has a food allergy which can be related to more than one allergen. To date, the most common food allergy is considered to be related to peanuts.

Most allergens are part of everyday raw materials, their use and contact with them can sometimes be inevitable. As such, a HACCP Allergen Control Program is an essential tool to uphold food safety in your organization. In this article, we will share the things you need to know when it comes to allergens and making an effective allergen control program.

Protecting allergic consumers is a critical duty of any food business. An effective allergen control program, as part of your HACCP plan, prevents unintended allergens from ending up in products and ensures all allergens are properly declared.

The stakes are high: undeclared allergens have become one of the leading causes of food recalls globally. In this comprehensive guide, we’ll cover how to build a robust allergen control plan, include a handy checklist/template, and answer common questions to help you manage allergens confidently.

What is an Allergen Control Program and why is it important?

An Allergen Control Program (or Allergen Control Plan) is a written, systematic approach that food manufacturers and restaurants use to identify, control, and prevent food allergens from causing harm. In practice, this program outlines how you handle allergenic ingredients from the moment they arrive (receiving and supplier info) through processing, packaging, and even cleaning procedures. It also covers how you inform consumers of allergens in your products (labeling). Essentially, an allergen control plan is a cornerstone prerequisite program to your HACCP food safety system, focusing specifically on allergenic hazards.

Why is this important? For one, food allergies affect millions of people. If an allergen ends up in a food unknowingly, the allergic consumer is at risk of serious reactions, even anaphylaxis. Regulators recognize this danger – that’s why laws require clear allergen labeling and controls.

Undeclared allergens are a top cause of food recalls in the US and abroad, accounting for nearly half of all recalls in recent years. Beyond consumer safety, failing to control allergens can mean regulatory violations, lawsuits, and damaged reputation.

Having a strong allergen control program protects your customers’ health and your company’s viability.

What are the 5 key goals of an Allergen Control Program?

The main goal of an effective allergen program is to prevent any allergen from contaminating products that are not intended to contain them and inform your consumers if any of your products may contain allergens. An effective HACCP allergen control plan should meet the following goals  in order to accomplish this aim:

1. Identify potential allergens

Begin by cataloging every ingredient and raw material used in your facility and determining which ones contain any of the major allergens. This includes reviewing supplier documentation, formulations, and even potential sources of cross-contact during ingredient sourcing and delivery. The more accurately you identify allergens, the more precisely you can build controls around them.

2. Prevent cross-contamination

Develop and implement strategies to avoid unintentionally transferring allergens to allergen-free products. This includes production scheduling, segregated storage, dedicated equipment or utensils, and validated cleaning procedures. Cross-contact can occur through surfaces, hands, air (in the case of powders), or rework, so your plan must address all these potential vectors.

3. Ensure accurate labeling

Product labels must clearly reflect any allergens present, using legally compliant formats such as “Contains” statements or bolded ingredients. This requires alignment between recipe formulation, production, and packaging. Establishing a reliable label review process and managing label inventory effectively are key to preventing mislabeling, which is one of the most common causes of allergen-related recalls.

4. Train employees

Staff should be trained not just on what allergens are, but how they apply to their specific roles—whether that’s receiving, storage, production, sanitation, or labeling. Reinforce training regularly, especially when new products, ingredients, or procedures are introduced. Well-trained employees are your first line of defense against mistakes that could lead to allergen cross-contact.

5. Document and review regularly

Allergen control is not a one-time setup. Keep records of all processes, including cleaning logs, label checks, training attendance, and supplier documentation. Set a schedule for regularly reviewing and updating your plan—especially when there are changes in ingredients, suppliers, equipment, or regulations. Documentation not only ensures consistency but also demonstrates compliance during audits or inspections.

Meeting these goals will not only help you comply with food safety regulations, but also demonstrate due diligence in keeping consumers safe from allergen hazards.

Major Food Allergens: US “Big 9” vs. UK/EU “Big 14”

One of the first steps in allergen control is knowing which foods/ingredients are considered major allergens that you need to manage and declare. Different countries have different lists of major allergens:

U.S. FDA “Big 9” Allergens

• Milk
• Eggs
• Peanuts
• Milk
• Tree nuts (e.g. almonds, walnuts, pecans)
• Soybeans (soy)
• Wheat
• Fish
• Crustacean shellfish (e.g. shrimp, lobster, crab)

• Sesame

• Celery
• Cereals containing gluten (e.g. wheat, barley, rye, oats)
• Crustaceans (e.g. crab, shrimp)
• Eggs
• Fish
• Lupin
• Milk
• Molluscs (e.g. clams, mussels, oysters)
• Mustard
• Peanuts
• Sesame
• Soybeans
• Sulphur dioxide and sulphites (at >10ppm)

• Tree nuts (e.g. hazelnuts, cashews, almonds) 

As the table shows, the U.S. FDA recognizes 9 major allergens that must be declared on labels (these are mandated by the Food Allergen Labeling and Consumer Protection Act and updates from the FASTER Act adding sesame)​. The U.K. and EU require labeling of 14 allergens, which include the U.S. list plus additional ones like celery, mustard, lupin, molluscs, etc.

It’s crucial to know which allergens are present in your ingredients. For instance, if you operate in the U.S., you’ll be focused on the Big 9, but if you ship products to Europe or serve customers in the U.K., you need to account for the Big 14. In practice, many companies just default to managing and labeling for the larger list to be safe.

Tip: Keep an updated Allergen Ingredient List in your facility. This could be a simple spreadsheet or binder section where you list every ingredient you use and mark which of the major allergens it contains (or if it’s derived from one). Include “contains X” label statements for each ingredient. This master list will be the foundation of your allergen control plan because it tells you what you’re controlling.

7 Key Components of an Effective Allergen Control Plan

Part of an effective allergen risk reduction program on your HACCP plan is ensuring that the correct control measures are in place. An allergen control checklist is most helpful to achieve this goal by following some considerations for a food manufacturing facility.

Building a HACCP allergen control program involves several components, each addressing a point in your process where allergens need to be managed. Below are the key components and best practices for each:

1. Allergen Management Team and Training

Establish a dedicated allergen control team or designate a coordinator (often part of the food safety/HACCP team). This team is responsible for developing, implementing, and updating the allergen control plan. It usually includes management (to ensure company commitment), quality assurance/food safety personnel, and representatives from production and purchasing.

Training is vital for all employees, not just team members. Train your staff on:

• Allergen Awareness: Teach what the major allergens are and the severity of allergic reactions. Employees should understand why strict procedures are necessary (e.g., a small amount of peanut residue could be life-threatening to someone).
• Handling Procedures: Instruct on how to handle allergenic ingredients safely. For example, using dedicated scoops or utensils for allergen-containing items, or wearing disposable aprons/gloves when dealing with allergens and removing them afterward.
• Avoiding Cross-Contact: Emphasize simple habits like washing hands and changing gloves between handling different foods, and not carrying ingredients on their clothing from one area to another.
• Label Reading: Staff who receive goods or mix ingredients should be trained to always read ingredient labels and formulations. They must catch if, say, a supplier sends a new formulation that includes an allergen (e.g., a spice blend that now contains wheat).

• Emergency Procedures: While prevention is the focus, train staff on what to do if there is an allergen exposure or a mislabeling is discovered (e.g., hold the product, notify supervisors immediately, etc.).

By having a trained team and workforce, you create a culture of allergen safety. Many facilities post reminders and have periodic refreshers. Remember, training isn’t one-and-done. Shedule refresher training at least annually or whenever procedures change. Document all training sessions (who attended, what was covered) as proof of your team’s expertise.

2. Supplier Review and Ingredient Control

Your allergen control efforts start even before ingredients enter your facility. It’s critical to work with suppliers who are transparent about allergen information. Key actions:

• Obtain Allergen Declarations: For every ingredient or raw material, have your supplier provide an ingredient specification sheet or allergen statement. This documentation should clearly state which of the major allergens (if any) the product contains and whether there’s a risk of cross-contact at the supplier’s plant. For example, a spice might not contain peanut as an ingredient but could be produced in a factory that also processes peanuts – you need to know that.
• Review Labels on Incoming Ingredients: Train receiving staff to check that incoming ingredient labels match what you expect. If a supplier sends a slightly different product or an updated formula, examine the label for any new allergen warnings. Retain ingredient labels (or copies) for all products you use – this is a good practice to quickly verify allergen info and is even a recommended part of allergen control plans (for instance, keeping labels on file is often highlighted in food safety training).
• Supplier Allergen Policies: Prefer suppliers who have their own allergen control programs. You might request proof or questionnaires about how they prevent cross-contact. If a supplier has weak allergen controls, you may need to test their ingredients or reconsider using them.
• Approved Supplier List: Maintain a list of approved suppliers for allergen-containing materials. If you need to use a new supplier in a pinch, have a procedure to vet their allergen info first. Changes in suppliers or ingredient formulation are moments of high risk for undeclared allergens, so handle them through a formal approval process.

By controlling allergens at the ingredient source, you eliminate surprises down the line. This step ties into your HACCP hazard analysis – every allergen that comes in should be identified as a potential hazard that you have controls for in the subsequent steps.

3. Storage and Segregation of Allergenic Ingredients

Once ingredients are on site, proper storage and segregation are fundamental to prevent accidental mixing or cross-contact:

• Dedicated Storage Areas: If space permits, use proper food storage practices and store allergenic ingredients in a specific area of the warehouse or a separate room. For example, have a designated rack or shelf for “Allergens: Milk Powder, Nuts, Wheat Flour etc.” separate from non-allergenic items.
• Color Coding and Labeling: Clearly label containers or ingredient bags that contain allergens. Many companies use color-coded stickers or bins (e.g., red tags for allergenic items, green for allergen-free). Some will even tag ingredients with the word “ALLERGEN” in bold. This visual cue helps staff instantly recognize that extra caution is needed with those items.
• Physical Separation: Store allergenic powders or liquids on lower shelves to avoid spilling or dripping onto other foods. Keep allergens in closed containers. For instance, if you have open bags of almond flour, keep them in lidded bins once opened. Ensure that tools like scoops are not shared between allergenic and non-allergenic ingredients (dedicate one scoop to the allergen, or use single-use scoops).
• Preventing Mix-ups: Never store allergenic ingredients above non-allergenic ones. Also, consider how you arrange like items – e.g., don’t place salt (non-allergen) in a similar-looking bag next to milk powder (allergen) where someone might grab the wrong one. Different packaging or clear labeling helps avoid these mix-ups.
• Allergen Equipment/Utensils: Ideally, have dedicated utensils, containers, or even processing equipment for major allergens. For example, some plants have separate color-coded measuring cups for allergen-containing ingredients. If dedicated equipment isn’t feasible, cleaning (next section) becomes even more critical.

By organizing your storage with allergen safety in mind, you greatly reduce the chance that an allergen will accidentally find its way into a product that shouldn’t have it. Segregation is a simple yet powerful preventative measure.

4. Production Scheduling and Cleaning Procedures

In the production area, careful scheduling and thorough cleaning are the main lines of defense against cross-contact:

• Schedule Smart: Whenever possible, sequence your production runs so that products with allergens are run last. For example, if you produce a non-allergen item and a peanut-containing item on the same line, produce the non-allergen item first, then the peanut item after. This way, if any traces are left behind, they won’t contaminate the next product (because the next product is actually one that already has that allergen). In some cases, it’s also wise to schedule a full cleaning right after running an allergen to prevent carryover to the next day.
• Allergen Changeovers: Plan for allergen changeover cleaning when switching a production line from an allergen-containing product to an allergen-free product. This often involves a complete washdown or cleaning protocol. Document these changeovers in your production schedule. For instance, note that after producing “Chocolate Almond Cookies” (contains tree nuts), a cleaning cycle is done before producing “Sugar Cookies” (no nuts).
• Sanitation Standard Operating Procedures (SSOPs): Have specific SSOPs that address allergen cleaning. Allergens can be stubborn; for example, allergenic proteins can reside in equipment crevices. Your cleaning procedure might include steps like a preliminary rinse, a detergent wash, a thorough rinse, and maybe a sanitizing step (bearing in mind sanitizers don’t remove allergens, they just kill bacteria – the physical removal via cleaning is what’s needed for allergens). Pay special attention to equipment like conveyors, mixers, ovens, and utensils.
• Cleaning Validation: How do you know your cleaning worked? Competitor best practices suggest validation and verification. Validation might mean initially testing the effectiveness: use allergen test kits (like ELISA swabs) on supposedly “clean” equipment to ensure no allergen residue remains. You might do this when first establishing your cleaning process or after equipment changes. Verification means on a routine basis, verify that cleaning crews followed the procedure (checklists, inspections) and perhaps periodically do spot tests. This is an advanced step, but it’s becoming more common in food industry to regularly test for allergen residues as part of verification.
• Avoiding Cross-Contact During Production: Beyond scheduling and cleaning, manage the environment: don’t let ingredients or dust travel. For example, if you’re grinding almonds, that area should be enclosed or far from where you make an allergen-free product to prevent airborne cross-contact. Use barriers or distance to separate production lines if possible. Also, control personnel movement – if workers must move from an allergen station to a non-allergen station, have them change smocks or gloves.

Effective scheduling and rigorous cleaning go hand in hand. Many allergen incidents trace back to inadequate cleaning (a bit of allergen was left on equipment). So, treat cleaning for allergens with the same seriousness as you would cleaning for bacteria in a ready-to-eat product – it’s that important.

5. Preventing Cross-Contact in Facility Practices

Cross-contact can occur through many little routes in a facility, so implement practices that block those routes:

• Utensil Management: As mentioned, dedicate or clean utensils between uses. Even things like forklifts or carts – if a pallet of allergen bags spills powder on a forklift, clean it before it’s used elsewhere.
• Rework Handling: Rework is reusing product or mix from one batch in another. If any rework contains an allergen, label it and store it as an allergen and only reuse it in products that have that allergen. Never mix rework from an allergen product into a supposedly allergen-free product. Many allergen recalls happen because rework with an allergen got into a product that didn’t declare it.
• Employee Practices: Encourage hand washing and tool washing between tasks. Disallow eating common allergen foods on the production floor (e.g., no peanut snacks in a peanut-free candy factory).
• Maintenance and Dust: If maintenance is done on equipment (like changing a filter or scraping down a mixer), ensure the area is cleaned afterward. Allergen dust can linger – for example, milk powder dust could settle on a surface and later fall into another product. Good ventilation and dust collection in areas where powders are handled can prevent spread.
• Facility Flow: If possible, design workflows so that allergen handling is somewhat contained. For instance, have a specific table or mixer that is used for allergen formulations, so you limit where that allergen goes. Control foot traffic: use footbaths or change shoe covers if employees move from an allergen station to a non-allergen station.

These practices, while sometimes seemingly minor, build layers of protection. They ensure that even outside of main production and cleaning, you’re not allowing allergens to hitchhike on tools, people, or rework into places they shouldn’t be.

6. Labeling and Packaging Controls

Even with all the cross-contact prevention, labeling remains a critical element. If a product does contain an allergen (intentionally or via unavoidable traces), the label must declare it clearly:

• Accurate Recipes and Labels: Maintain an updated record of every product’s recipe and corresponding label. Whenever a recipe changes or you add a new ingredient, immediately review if the allergen information on the label needs to change. One good practice is having an ingredient change log and doing a quick allergen check for any change. For example, if you switch a spice brand and the new one has mustard, you must update the label.
• Label Review Process: Institute a label review checkpoint either at packaging or as part of final QA. This means someone verifies that the correct label is on the product and that the allergen declarations (the “Contains: …” statement or allergen bolded in ingredient list as per regulations) match the product’s ingredients. This step can catch errors like an allergen-containing product in the wrong package. Retaining label proofs and having a library of current approved labels for each product can be very helpful​.
• Prevent Label Mix-Ups: Only have one type of label out on the line at a time to avoid mix-ups. If you just finished packaging Product A and are about to start Product B, remove or secure leftover labels from Product A. Many recalls occur because the wrong label was applied (e.g., a product containing eggs got packaged with a label that didn’t list eggs). Strict label control procedures (like using barcode scanners to verify label-product match, or having QA sign off on label changes) add safety here.
• “Allergen may be present” Warnings: Sometimes despite best efforts, there is a risk of cross-contact that can’t be fully eliminated. In such cases, companies use precautionary allergen labeling like “May contain X” or “Made in a facility with Y”. Use these warnings judiciously and honestly. They should not be a crutch for poor control (“may contain” should not excuse you from cleaning properly), but rather a last informational step if a low-level risk might remain. Overusing precautionary labels can erode consumer trust and limit who can eat your product, so it’s best to have solid controls so you rarely need to use “may contain” statements.
• Regulatory Compliance: Ensure your allergen labeling complies with the local regulations – e.g., in the U.S., allergens must be listed in plain language either in the ingredients or in a contains statement; in the EU, the 14 allergens must be emphasized (often bolded) in the ingredient list. Having a compliance checklist for labels (correct allergen names, format, etc.) is a good idea.

Ultimately, even if an allergen accidentally gets into a food, a correct label can protect consumers by alerting them. It’s your final safety net. So treat label control as seriously as any critical control point – double-check and document it every production run.

7. Documentation, Verification, and Regular Review

An allergen control program is only as good as its execution and maintenance. This means you need to document what you do and continuously improve:

• Record-Keeping: Keep records for all the above activities. This includes:
  • Ingredient allergen spec sheets from suppliers (and updates when they change).
  • Cleaning logs and checklists (signed off by sanitation crew and verified by a supervisor).
  • Production schedules showing product sequencing and changeover cleanings.
  • Allergen test results (if you conduct ATP or ELISA swabs for allergen residues).
  • Training records and attendance.
  • Label verification checklists from each batch or lot.
  • Internal audit findings (if you audit your allergen controls). These records prove that procedures are being followed and are invaluable if there’s ever a question or an external audit.
• Internal Audits & Verification: Periodically audit your own allergen control plan. Perhaps quarterly or at least annually, have the allergen team do a walkthrough: Is everything still being done as written? Are there any new risks? You might catch, for instance, that a new ingredient was introduced but an old SOP wasn’t updated to include its allergen.
  
  Additionally, verify that controls are effective – e.g., check a “clean” non-allergen product for allergen presence via testing once in a while (finished product testing). Some companies include allergen checks in their routine quality testing, especially for very sensitive allergens like peanuts.
• Review and Update the Plan: Review the allergen control plan at least annually (often during an annual HACCP plan review)​, and whenever there’s a significant change:
  • New product or ingredient (does it introduce a new allergen?).
  • New equipment or process (does it create new cross-contact points?).
  • New supplier or formula changes (verify their allergen status).
  • Regulation updates (for example, when the U.S. added sesame as an allergen in 2023, plans needed updating to include sesame controls).
  • Any allergen incident or close call (if something goes wrong or almost wrong, update procedures to prevent recurrence.

During review, involve cross-functional staff (i.e., the people who do the receiving, mixing, cleaning, etc.). Their experience can identify practical improvements. For example, an employee might note, “We need a better way to mark opened allergen bags,” leading you to introduce a new tagging system. That kind of frontline experience is gold for refining your plan.

Finally, management support must continue for the allergen program. Leadership should sign off on the allergen policy and ensure resources (like cleaning time, testing kits, extra label stock, etc.) are available to keep the plan effective. Allergen control is an ongoing effort, not a one-time setup. When properly maintained, it greatly reduces the risk of allergic reactions and costly recalls.

Allergen control plan checklist

Every facility’s allergen control plan will differ slightly, but most will contain common sections. Using a template can help ensure you don’t miss any critical components when drafting or updating your plan.

Below is an Allergen Control Plan checklist outlining typical sections and tasks:

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For a more formal template, industry organizations like the International Dairy Foods Association (IDFA) provide allergen control plan templates, and regulatory bodies like the FDA have guidance documents with examples. Tailor the template to your facility’s needs: for a small bakery, the plan might be a few pages covering the basics; for a large manufacturer, it could be much more detailed with separate appendices.

Checklist usage: Consider turning the critical points into a checklist for daily/weekly use. For example, a Daily Allergen Control Checklist for a manager might include items like:

• Ingredients verified against recipe
• Equipment cleaned and inspected before non-allergen run
• Correct labels applied and double-checked

This operational checklist helps ensure the written plan is executed every day.

By having a clear template and checklists, you create a system that is easier to follow and audit. It moves allergen control from concept into routine practice, which is ultimately what protects consumers consistently.

Following this guide and continuously improving your approach will help ensure your HACCP allergen control program significantly reduces the risk of allergen-related issues.

Always remember: the goal is to keep your consumers safe and confidently enjoy your products without worry. An effective allergen control plan, executed daily, is how you achieve that safety and trust.

How to easily implement and manage your HACCP allergen control program

From the hospitality to the healthcare industry, food businesses must have an effective allergen control program as a prerequisite for their HACCP plan. To build one, a thorough assessment of the whole production process from ingredients to distribution is a must.

At FoodDocs, we help you build your HACCP allergen control program to strengthen your food safety credibility by using the most efficient HACCP software.

This development by FoodDocs guarantees an effective allergen program in just an hour or less. Learn which areas are critical points when it comes to allergen contamination and their potential risks.

You can try FoodDocs' full suite of food safety management software with a free 14-day trial or book a personalized demo to see how we can support your allergen control program needs.

Frequently asked questions about allergen control