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Handling, Storage, & Transport

Protecting Organic Products During Transport, Receiving, and Shipping

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5.2 Version 1 August 4, 2026

As a handler, it’s your job to protect organic integrity once a product or ingredient is in your hands, that’s what lets customers trust the label and what you produce. This means paying close attention at every stage, whether you’re receiving organic ingredients, storing them, or transporting finished products. Even a small mistake, like accepting a delivery in a truck that wasn’t cleaned properly or storing organic grain next to treated seed, can cause a product to lose its organic status. This article walks you through the basics of receiving, handling, storing, and transporting organic products, and the records you’ll need to keep along the way.

What You'll Learn

  • Buyer’s and seller’s responsibilities regarding transport
  • When transporters need to be certified organic
  • Requirements around cleaning, recordkeeping, and verification
  • Risks for contamination and commingling during transport
  • Best practices and procedures for receiving product into your facility

The organic label depends on consumer trust, which makes maintaining the integrity of organic products a responsibility shared by everyone in the supply chain. As products are transported to your facility and received, numerous points of vulnerability can put their certification status at risk. If a product is contaminated or commingled with nonorganic materials before it arrives or during unloading, it can no longer be sold as organic.

Fortunately, there is a practical way to get ahead of these risks: Organic Control Points (OCPs). OCPs are the specific points in your process where contamination or commingling is most likely to occur. By identifying these points, you can examine them closely and adjust your processes to reduce the risk. Best practice is to identify OCPs during the planning stage of your handling processes, when root causes are easiest to address.

Transport

Transportation is the movement of product between a seller and a buyer, and sound communication among everyone involved is what keeps organic integrity intact along the way. Clearly identifying and documenting who is responsible for maintaining organic integrity during transport, and what is required of those handling your ingredients and products, helps mitigate risk and ensures responsible procedures are followed at every step. While sellers and buyers share ultimate responsibility for upholding organic integrity during transport, clearly defining each party’s role is what manages the risk of commingling and exposure to prohibited substances.

Sellers are typically responsible for arranging transport in a manner that does not compromise organic integrity, and for providing complete records to the buyer, including the invoice, bill of lading, and organic certificate.

Buyers, in turn, are typically responsible for verifying the organic status of the product upon arrival, evaluating transportation risks for contamination and commingling, and obtaining audit trail documentation back to the last certified entity.

Business arrangements between buyers and transporters can take many forms, including buyer-owned or seller-owned transport. Whatever the arrangement, it is essential to identify and document which party is ultimately responsible for organic integrity during transport.

Does Your Transporter Need to Be Certified?1

Whether a transporter is required to be certified organic is rooted in the risk of contamination or commingling while the product is in their possession. The USDA regulations require operations to be certified based on the activities they perform and the type of packaging or containers the product is in while in their possession. It is important to know whether your transporter is required to be certified, and the documentation that you must collect from them based on their status.

Transporters generally do NOT need to be certified if they:

  • Simply transload between forms of transport, not including to and from storage;
  • Only move sealed, tamper-evident packaged and containerized organic products; or
  • Only load and unload bulk shipments at organic facilities, such as a delivery directly from a certified farm to a certified processing facility.

Transporters generally DO need to be certified if they:

  • Perform any other handling activities like combining, containerizing, or repacking; or
  • Load or unload at nonorganic facilities.

Even if a transport company is exempt from certification, they can choose to be certified. Operations that do not require certification must still follow the rules for handling organic products. They must still prevent the contamination and commingling of organic products, verify and document the status and quantities of the organic products, and keep all records necessary to document compliance with these requirements.1 As usual, contact your certifier if you are uncertain.

Vehicle and Container Requirements

To prevent contamination with prohibited substances and to prevent commingling organic with nonorganic products, most transport vehicles or containers must be cleaned before transporting organic products. This can look different for different types of product and vehicles. The regulations adapt to the situation around the level of risk. For example, a box truck carrying packaged goods, a tanker truck carrying fluid milk, and a grain truck carrying bulk grains each require different cleanout methods. Whichever cleaning method is most appropriate, all need to be cleaned to prevent commingling and contamination.

It is your responsibility to ensure that any product that you ship or receive has been transported in a properly cleaned vehicle or container. A clean truck affidavit, or other documentation of cleaning, is a common method of documenting that equipment was properly cleaned when transporting bulk products that are not in impermeable packaging, such as bulk grain. Clean truck documentation should accompany the load to the buyer for your records.

Clean truck documentation may not be needed if the organic ingredient is arriving via the common mail system or encased in impermeable packaging in a truck full of other packaged goods. Buyers should inspect the arriving transport vehicles for risk, and include how they verify the incoming transport is clean in their Organic System Plan.

Loading and Unloading Procedures

Unloading, especially with tight schedules, can easily lead to commingling in areas that handle both organic and nonorganic products. Carefully think through the unloading process, staff training, and required documentation to avoid issues. Your certifier will be assessing risk and will ask you for your SOPs for transportation. Consider the following examples:

  • A cottage-scale processor went to a neighbor’s organic farm and picked up four boxes of fresh tomatoes to make salsa and loaded them into a pickup truck. The risk will depend on whether the boxes are open, whether the truck is open, and what else is riding in the truck with the tomatoes.
  • A feedmill receives grain, which is dumped into a pit and then augered and elevated into a grain silo. The dump pit, grain auger, and elevator are high risks for commingling if the feedmill also uses them to handle nonorganic grain or ingredients.

Transporting Mixed Loads

If both organic and nonorganic products might be transported together, then there is a real risk of commingling. Packaged products will have a lower risk than bulk or more open containers, like crates. The highest risk would be transporting both organic and nonorganic products that are visually indistinguishable in open-top containers. If you receive products from transporters who carry mixed loads of organic and nonorganic products, it is your responsibility to require them to practice spatial segregation within their truck.2,3 For example, if open flats of nonorganic tomatoes are stacked above open flats of organic tomatoes, commingling could occur on a bumpy delivery route with nonorganic tomatoes falling into flats of organic tomatoes. In this way, the physical practices used to prevent allergen commingling are helpful when identifying physical practices to prevent commingling of organic and nonorganic products.

Receiving

To a certain extent commingling and contamination are out of your hands when your organic ingredients are being transported to you, but as they are received at your facility there are several risks you’ll need to avoid. Receiving staff can ensure that you don’t receive any organic products that were mixed with nonorganic products by inspecting delivery trucks and vessels before accepting a delivery. These inspections can identify any potential for commingling during transportation so that receiving staff can reject any delivery that could have caused commingling.

Once product arrives at your facility, you must establish a procedure to immediately distinguish organic and nonorganic products at the point of unloading, before they enter into your product flow.3 This step serves as a crucial organic control point, especially if you are receiving identical organic and nonorganic products (e.g., flats of organic and nonorganic strawberries, barrels of organic and nonorganic apple cider vinegar, totes of organic and nonorganic grain), where the risk of commingling is high.2 Without clear identification at receipt, nonorganic ingredients may be accidentally selected for use during production.

Receiving staff can prevent this risk by verifying each delivery before it is accepted or moved into storage. This verification should include confirming that the bill of lading (BOL) matches the physical shipment, that organic items are clearly identified on both packaging and paperwork, that lot codes are present for traceability, and that quantities are accurate. It can also include reviewing the current supplier organic certificate to confirm that any organic products received are covered under certification and properly listed.

Tips for Receiving Organic Shipments

Verify the product:

  • Check that the product labeling matches the shipping documents.
  • Check the labeling for nonretail containers, they must:4
    • Be labeled as organic.
    • Have a production lot number, shipping identification, or other unique information that links the container in an audit trail.
  • Obtain a copy of the supplier’s organic certificate and addendum. You can use the USDA’s Organic Integrity Database to find it.5
    • Make sure the certificate and addendum clearly match the shipping documents, unique identifier, and organic identifier.
      • Operation Name and Address;
      • Documents are valid and standard;
      • Issue date is within 12 months of receiving the product; and
      • The specific product is listed.

Verify shipping documents:

  • Shipping documents, like bill of lading, manifest, and invoice, must identify the product’s organic status and be traceable back to the last certified operation.6

Inspect for contamination and commingling risk in the transportation vessel:

  • Inspect packaging for signs of damage, moisture, foreign debris, or prohibited substances.
  • Inspect the vehicle for any evidence of contamination or commingling.

If your product is bulk or unpackaged:

  • Verify if there are any nonorganic products in the same truck or vessel, like a barge or train, and assess for commingling risk.
  • Obtain documentation of cleaning before organic transport, such as a Clean Truck Affidavit, supplied by whoever is responsible for transport.
  • Inspect the delivery vessel for any obvious signs of inadequate cleaning.
  • Ensure that your receiving areas are clean and ready to unload organic product. Bulk receiving equipment such as dump pit, augers, bulk liquid links, and storages are of particular concern for cleaning.
  • If you receive product in sealed trucks, verify the seal number against shipping documents and confirm the seal is intact before breaking it.

Document the shipment in your records:

  • Record all lot numbers on arriving organic products.
  • File all paperwork according to your OSP.

When we receive the product, we look at the invoices and make sure they say organic. We look at the actual product itself to make sure that those lot codes match what the invoice says … And then after that, we put it on the receiving log, and in that receiving log we automatically link that certificate of analysis and the invoice to that receiving log online.

Michelle PusateriFounderNana Joes Granola

It is also important to ensure that your facility is ready to receive organic product at the moment of delivery. Ensure that the receiving dock or equipment is properly cleaned and prepared to accept the organic product. This is particularly important when receiving bulk product into mixed-use facilities where the equipment used to move the product can be a source of cross-contamination and commingling. Dump pits, augers, bulk tanks, pipes for liquid products, and storage vessels all must be thoroughly cleaned and prepared prior to unloading the bulk organic product from the delivery vessel.

Plan for When Things Go Wrong

As you are inspecting your organic products at receiving, have a plan for what you will do if you find an issue. At minimum, you must document the issue and divert the rejected load from organic use. Some handlers have a holding area for the delivered product until it is verified. Document your verification procedures and outcomes. If you quarantine unverified products, document your release procedures so they can be easily audited by your inspector.

Shipping

Commingling risks do not end at receiving, storage, and production. They must also be controlled during shipping of finished products, particularly for mixed-use handlers who ship products in open containers. As with receiving, shipping should be treated as an organic control point where organic and nonorganic products are clearly identified, verified, and kept fully separate.

Applying the same principles used in receiving, shipping staff should confirm that all outbound organic shipments are correctly labeled, match the shipping documentation, such as the bill of lading, and are supported by proper traceability and lot coding. Organic products should be physically segregated from nonorganic goods in staging and loading areas, with clear visual indicators and procedures to prevent mix-ups during final pallet assembly and truck loading. Just as incoming products are verified before entering the facility, outbound products should be verified before they leave it, ensuring that only correctly identified organic products are shipped as organic.

Lot Identification and Traceability

For the sake of organic integrity, handlers need to be able to track their products from receiving through storage, processing, and shipping. When they arrive at your facility, your ingredients should have an associated lot number on the shipping documents (and nonretail label, as applicable).

Many handlers clearly mark organic product while it’s in their facility in order to reduce risk. If you are applying organic labeling or signage to your products, document the labeling in your records.

If you do little to no processing, you might be able to use the original lot number or make a minor addition to it, and track your ingredients/products using this same lot number until they are sold. However, your recordkeeping system may use different lot numbers at different stages of processing. Whatever your system, it starts at receiving, and you must be able to trace your final product back to the lot number of each received ingredient.

Conclusion

The moment an organic product leaves a farm or supplier and heads your way, the clock is ticking. You can’t control every bump in the road, but you can control what you require before that truck pulls up, what your team checks when it arrives, and what happens if something doesn’t look right. A solid receiving procedure doesn’t have to be complicated; it just has to be consistent. Get the documents, check the load, log what you received, and make sure the lot number follows that product from your dock all the way through your process. Do that every time, and you will have done what you can to protect the integrity of your organic products.

Action Items

  • Tell your transporter exactly what you need to verify before the load ships.
  • Check whether your transporter needs to be certified.
  • Build a receiving checklist and use it.
  • Identify the organic control points in your transport and receiving process.
  • Decide in advance what you’ll do if something looks wrong at receiving.
  • Make sure every incoming shipment has a lot number you can track.
  • Document your receiving and shipping procedures in your OSP.

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