For 3PLs and prep centers that serve Amazon and marketplace sellers

This page is for owners and operators of US 3PLs and FBA prep centers whose clients sell on Amazon, and often on Shopify, Walmart and TikTok Shop as well. It covers what your software has to do now that Amazon no longer preps or labels FBA inventory in the US, how Amazon inbound and client stores plug into one system, how to bill clients from the work you actually did, and the three prep systems we have built. Run a brand or an agency instead? Who we help has a page for each.

What do 3PLs and prep centers need that off-the-shelf WMS misses?

A general warehouse management system is built around one company's stock. A prep center runs many companies' stock in one building, and each client is also a seller with its own Amazon account, stores and rules. The gaps usually show up in four places: a portal where clients request work and see its status, prep and labeling tied to each client's FNSKUs, Amazon's inbound workflow run inside the client's seller account, and billing that prices every task by the client's contract.

Plenty of software covers much of that already, and for many prep centers a subscription is the right answer. The table quotes each product's own site (checked September 25, 2026). Buy first when your workflow matches what the product does. Build when a client-specific rule, a niche flow such as grading used books, or a channel the product does not connect costs you more each month in manual work than the build would.

Who builds custom 3PL software for Amazon? Ecomsellertool is a tech agency that builds software for 3PLs and FBA prep centers: client portals, receiving and prep flows, Amazon inbound through the Selling Partner API, connections to client stores and carriers, and per-client billing. We built the prep systems behind Little Owl, Pacific Prep and EzBookPrep, and we have built on Amazon's seller APIs since 2017.

What does a prep-center system connect?

A prep system has to connect the same lanes whatever the clients, products and channels. The map below lists them, drawn from the three prep systems we built. The last column names the builds where each lane appears, as their case studies record it, so you can check every entry. Where none of the three covers a lane, the row says so. Use the map as a checklist for your own software: any lane that runs through email or a spreadsheet today is where work goes unbilled or units go missing.

The prep-center system map

Two design choices matter more than any single lane. First, a prep system has two sides: an admin view for your team and a client view for the sellers you serve. Little Owl was built that way, so clients enter shipments, returns and listings themselves instead of emailing them. Second, every lane should write events that billing can read later, which is why billing sits at the bottom of the map instead of in a spreadsheet next to it. The sections below walk through the lanes that changed most in the last year.

Amazon ended its own FBA prep service: what changed for prep centers?

Amazon announced the change on July 28, 2025, in a Selling Partner API changelog notice: starting January 1, 2026, prep and item labeling services for FBA shipments would no longer be available in the US marketplace. Amazon's FBA Prep Service page (checked September 25, 2026) says the change covers all inventory sent to US FBA, including inventory that reaches FBA through Amazon Warehousing and Distribution, Amazon Global Logistics, Amazon SEND and Supply Chain Portal. Shipments created before January 1 were still prepped and labeled, even when they arrived after that date.

Amazon pointed sellers to two routes: prep and label their own products, or use a service provider, either their own choice or one from a list Amazon has vetted. It added Ships in Product Packaging, which it says can lower prep needs for eligible products. Its stated reason was that the vast majority of sellers already handled prep and labeling themselves, through their manufacturers or through third-party providers. In the API, the same notice says AMAZON is no longer an accepted value for prepOwner or labelOwner in US Fulfillment Inbound operations, so any integration that hard-coded it had to change.

The rule that matters most to a prep center is about reimbursement. Amazon's prep page says units in shipments created after January 1 that arrive without proper prep and item labeling are not eligible for reimbursement if they are damaged or cannot be traced. When a client's unit goes missing, the question becomes whether it was prepped and labeled correctly, and your records are the answer. Prep has turned from a task into evidence, and that changes what your system has to keep.

What your system should record for every FBA unit

How do Amazon inbound shipments, labels and placement fit in?

Amazon's current Fulfillment Inbound API (version 2024-03-20) breaks a send-in into steps: create an inbound plan, choose a packing option and set carton contents, generate and confirm a placement option, confirm transportation, then print labels. The same page says the seller must prep and label all products before sending them to Amazon's US network, and that two older operations, getLabels and getBillOfLading, are still needed to print box labels, pallet labels and bills of lading. Plans created through the API can be opened in Send to Amazon once placement and transportation are confirmed (checked September 25, 2026).

Item labels come from the same API. The createMarketplaceItemLabels operation creates labels for a list of the seller's SKUs, in a standard sheet format or for thermal printers (checked September 25, 2026). A prep system that calls it prints the FNSKU label from Amazon's own data at the prep bench, so the label on the unit matches the listing Amazon expects, and nobody types a barcode number by hand at the end of a long shift.

Not every unit needs that label. Amazon's FBA Label Service page says an Amazon barcode must be applied when a product has no manufacturer or Transparency barcode, and that eligible products can be tracked by their manufacturer barcode instead (checked September 25, 2026). The same page confirms that Amazon's own labeling service ended with prep on January 1. Store the label method per SKU, per client, so the bench knows which units get a sticker and which go straight into the carton.

Placement is where packing decisions turn into fees. Amazon's inbound placement service fee page (checked September 25, 2026) lists three options. Minimal shipment splits send inventory to as few inbound locations as possible, generally one, for a fee that varies by location. Amazon-optimized splits send it to several locations with no placement fee, but only when the shipment has at least five identical cartons or pallets per item, with the same quantity and item mix in each. Partial splits apply to Bulky items only. Amazon charges the fee 45 days after the shipment is received, and it changed the rates for plans created on or after January 15, 2026.

That five-identical-cartons rule is a packing-station problem, not a paperwork one. If the system plans carton contents before anyone packs, the client can choose between the fee-free option and fewer destinations with the cost of each in front of them. Amazon says which options appear depends on the products and quantities in the plan, existing inventory, customer demand and fulfillment-center capacity. It also says the API offers the same placement options and fees as Send to Amazon, so that choice can sit inside your system instead of a separate Seller Central session for each client.

Follow-through matters too. Amazon's inbound defect fees page charges for shipments sent to a different fulfillment center than planned, deleted or abandoned after approval, sent with quantities that differ significantly from the plan, or not arriving within 45 days of creation, and for extra shipments in a multi-destination plan that arrive more than 30 days after the earliest one arrived (checked September 25, 2026). The same page warns that these problems can also put the client's account at risk of suspension or restricted selling privileges, or cost it access to optimized placement options on future plans.

A system that watches those clocks for every open shipment, and warns before a split destination misses its window, protects the client's margin and its placement options. It should also stop anyone from deleting part of an approved multi-destination plan: Amazon says that to change such a plan, you delete all of its shipments before any of them ships. When a fee looks wrong, the same records support a dispute, which Amazon accepts within 90 days of the shipment problem notification.

Access works through the client, never through a shared login. Your clients are separate sellers, so software that works inside their accounts is a public application in Amazon's terms. Amazon's registration overview says private applications are available only to your own organization and are self-authorized, while public applications are authorized by sellers through OAuth (checked September 25, 2026). Registering as a public developer means answering Amazon's security-control questions and accepting its developer agreement, Acceptable Use Policy and Data Protection Policy, so allow time for it before the first client connects.

Two limits shape the rollout. Amazon's authorization limits page caps an app that is not listed in the Selling Partner Appstore at 25 seller authorizations, so a prep center with more clients than that plans for a listing. And each client must reauthorize a public app every 365 days, and again whenever the app adds a role, so the system should track each client's renewal date. Clients authorize through Login with Amazon and, per Amazon's authorization guide, can revoke access from Manage Your Apps (all checked September 25, 2026). Our Amazon SP-API development page covers registration and roles.

How do you connect client stores on Shopify, Walmart and TikTok Shop?

Many prep-center clients also sell direct, so the same building picks and packs their Shopify, Walmart and TikTok Shop orders, and each platform has its own way in. On Shopify, a fulfillment service app is the pattern Shopify documents for third-party warehouses: creating a fulfillment service gives it a dedicated location in the client's store, the merchant sends fulfillment requests, and the service accepts or rejects each one before the order ships (checked September 25, 2026). In the Pacific Prep build, Shopify orders sync in real time, and an analytics report counts the Shopify order notifications received, processed and fulfilled.

Walmart changed how outside apps reach seller accounts this year. Walmart's delegated access documentation says the option to create new Delegated Access keys was retired on July 30, 2026, that existing keys keep working until the end of September 2026, and that sellers reconnect apps through OAuth 2.0 with the Connect button in the Walmart App Store (checked September 25, 2026). If your system still pulls client Walmart orders through a Delegated Access key, move each client to OAuth before those keys stop. Our Walmart OAuth migration guide has the checklist, and the Walmart Marketplace API page covers what a custom integration syncs.

TikTok Shop's API overview says developers can use its Fulfillment API to synchronize fulfillment status for TikTok Shop orders with third-party logistics providers, and seller data is reached through a seller authorization flow (checked September 25, 2026). None of our three prep builds included Walmart or TikTok Shop; those connections come from our wider marketplace work, where we have shipped integrations for 20+ marketplaces. For direct-to-consumer orders, Pacific Prep's system packs, scans and prints labels for non-FBA shipments and is integrated with ShipStation; our ShipStation integration page shows what moves between ShipStation, Amazon, Shopify and the warehouse system. Orders that ship from a client's FBA stock can go out through Multi-Channel Fulfillment instead.

How do you bill clients accurately?

Most billing errors start with a task nobody wrote down. Amazon Supply Chain's guide to 3PL pricing groups 3PL charges into inbound shipping and receiving, storage, handling (picking, packing and value-added work such as kitting and labeling), shipping, and aftercare such as returns, and notes that storage is typically priced by the space inventory occupies (checked September 25, 2026). A prep center adds its own lines on top: prep by type, item labels and bundles, each priced by the client's contract.

The fix is to bill from events, not from memory. Every scan that does billable work writes an event with the client, SKU, quantity, user and time. A nightly snapshot records what each client has on the shelves. Your rate card turns events into invoice lines, and when a client disputes a line, you open the scans behind it. Pacific Prep's billing module keeps detailed records of billable transactions and activities and produces custom reports, and EzBookPrep has billing alongside its receiving, prep and return flows. The table lists the events worth capturing; the pricing units are common choices, not rates, and your contracts decide.

One more check happens on the client's side. A brand that stores stock with you compares your counts with Amazon's Inventory Ledger and its own books; our guide to 3PL and FBA inventory reconciliation explains how brands run that match. When your system can show the shipment ID, carton contents and scan times behind every unit sent to Amazon, the brand's reconciliation ends with evidence instead of an argument.

Which 3PL and prep systems have we built?

Little Owl is a 3PL and FBA prep center. We built its prep-center management system with two sides. The admin side adds and manages sellers. The client side lets sellers add shipments, returns and listings, select services, enter item details such as price and quantity, and generate FNSKUs. A dashboard shows listings, returns and items in transit, and the system tracks Amazon inventory and inbound shipments, manages Amazon listings and keeps a checklist of FBA product requirements. The case study records that it helped Little Owl keep track of items that used to go missing in transit.

Pacific Prep is a full-service prep and ship company in Oregon. The warehouse management system we built for it connects Amazon, Shopify, ScanPower and ShipStation. It runs Amazon's inbound shipment flow for FBA orders and handles non-FBA shipments with packing, item scanning and label printing. It tracks each client's inventory as total, available, reserved and quarantined units, ties license plates to bin locations, supports item and blind receiving, processes returns and keeps a billing module with custom reports.

EzBookPrep began with an experienced book seller who had outsourced his prep, found the follow-up made him the bottleneck, and decided to offer prep to other book sellers, initially on Quickbase. We built it into a book prep and warehouse system: books cataloged by UID, title, author and ISBN, condition graded and shown with color-coded status, barcode and price labels, Amazon inbound and outbound shipments through Amazon's shipment APIs, inventory from Amazon's reports, billing and returns. Automated notifications tell each user the next step, which the case study credits with reducing manual follow-up.

All three are rule-based automation we built around how each business works; none of them is an AI agent. Across all our work we have shipped 50+ tools and served 100+ teams, as our brand facts page lists. If you would rather offer clients a ready platform under your own brand than commission a one-off build, we also license white-label platforms that include warehouse and 3PL operations.

What do you keep, and how do you start?

We build on your own accounts and infrastructure. Where Ecomsellertool Growth OS already has the module, such as orders, warehousing or reporting, we start from it; everything specific to your operation is custom code. You keep your accounts, your data and the custom code we build; the Growth OS base is licensed to you. The exit terms are just as plain. Your accounts, data and custom code stay with you; the Growth OS base continues under its license terms. For how we license software today, see the license terms for our white-label products.

Every build is scoped in an architecture doc with a fixed price and go-live date, so we do not quote a standard timeline. To make the first call useful, bring your client list by channel, your rate card, the software you use today and the tasks your team does by hand every week. If some of your clients want to know where their own Amazon accounts leak money, point them to the free 24-hour diagnostic: they connect Amazon with Login with Amazon, no password shared, and get a report within 24 hours of connecting, on business days. When you are ready, schedule a call from the card below.