Buy with Prime puts the Prime badge and Amazon checkout on your own Shopify store. For a brand that already ships Shopify orders through a 3PL, the practical questions are who ships the Prime items, how to keep both systems from shipping the same order, and how much stock has to sit in FBA.
Buy with Prime works alongside a 3PL by splitting your catalog: Prime-enabled SKUs ship from FBA inventory through Amazon Multi-Channel Fulfillment, and everything else ships from the 3PL. Amazon assigns Prime items to their own Shopify location, so the 3PL's integration must skip them. As of October 2026, Amazon charges a 3% Prime service fee plus a per-unit fulfillment fee, for 1 to 2 day delivery.
How does Buy with Prime work on a Shopify store?
You install Amazon's MCF and Buy with Prime app, choose which products offer Prime, and shoppers who are Prime members check out with their Amazon account. You do not need to sell on Amazon.com, but you do need FBA set up and inventory in Amazon fulfillment centers.
Shopify's Buy with Prime help page lists the requirements as of October 2026:
- Store: based in the US, selling in USD and shipping domestically, on an active Basic plan or higher, using the latest version of checkout.
- Payments: Shopify Payments active, with Amazon Pay turned on in the Wallets section.
- Amazon: an active Professional Seller Central account with Fulfillment by Amazon set up. Activating Amazon Pay through Shopify Payments creates a Seller Central account automatically.
- Checkout: split shipping turned on in Settings, Shipping and delivery, so shoppers can buy Prime and non-Prime items in one checkout.
Buy with Prime orders sync into Shopify with a Buy with Prime tag, and payment arrives in your next Shopify Payments payout. The app listing is free to install, built by Amazon, and rated 3.7 from 103 reviews as of October 30, 2026; two recent reviews report wrong inventory counts and changed shipping profiles, so test it on a few SKUs first.
Who fulfills Buy with Prime orders?
Amazon does. Once MCF is activated, orders placed through Buy with Prime are automatically fulfilled by Multi-Channel Fulfillment from your FBA inventory, and Amazon syncs the tracking numbers back.
Amazon's Buy with Prime FAQ adds three points that shape the 3PL setup:
- One shared pool: every channel that uses Amazon's fulfillment services draws on the same inventory. A Buy with Prime sale on your site and an Amazon.com sale take units from the same FBA stock.
- Live inventory checks: Buy with Prime checks stock when the shopper clicks the button and again at Place order, and reserves the units for 10 minutes. If FBA is out, the shopper is told the item is not available with Prime.
- Product must be in FBA: the button only renders for products that are fulfilled by Amazon and have non-zero inventory in Amazon fulfillment centers.
Your 3PL's inventory does not count for Buy with Prime. If a Prime-enabled SKU is out of stock in FBA but sitting on a shelf at your 3PL, the shopper sees the standard checkout for that item.
How does a 3PL fit into a Buy with Prime store?
The 3PL ships every item that is not fulfilled by Amazon, including the non-Prime items in a mixed cart. The main risk is double fulfillment, where the 3PL also picks and ships a Prime item that Amazon is already shipping.
Amazon's guide to third-party order management integrations explains how to prevent it:
- Separate locations. The app assigns Prime items to a fulfillment location named "Buy with Prime" or "Amazon Fulfillment". Any OMS or 3PL connector that routes Shopify orders should exclude both location names (or their location IDs) from what it fulfills.
- Use fulfillment orders. Amazon recommends that integrations read the assigned location on each Shopify fulfillment order. Older integrations that read the deprecated line-item fulfillment_service field are a risk, because one order can be split across several fulfillment orders.
- Allow SKU sharing. The app adds a second location under each Prime SKU. If a connector sets permitsSKUsharing to false, Buy with Prime cannot add its location; it must be true.
- Check your OMS. Shopify's own order management needs no changes. Amazon lists setup steps for ShipStation, Pipe17, WebBee, ShipHero, NetSuite (FarApp) and Brightpearl, says ShipBob needs no action, and lists Veeqo and Dianxiaomi as not compatible.
If your 3PL connects through Shopify's fulfillment order model, the split usually works without custom code. For how that model moves orders and tracking, see how Shopify syncs orders, inventory and tracking with a 3PL. Test a mixed cart (one Prime item, one non-Prime item) before launch and confirm that only the non-Prime item reaches the warehouse.
What does a Buy with Prime order cost in October 2026?
Three charges apply per order: a Prime service fee of 3% of order value (minimum $0.30), a fulfillment fee per unit, and payment processing. FBA storage applies to the inventory as well.
Amazon's Buy with Prime pricing page publishes a 2026 peak rate card effective from October 15, 2026. Selected per-unit fulfillment fees:
| Size tier and weight | 1-unit order | 2-unit order (each unit) | 3-unit order (each unit) | 4+ unit order (each unit) |
|---|---|---|---|---|
| Small standard, 8 oz or less | $6.61 | $4.33 | $3.55 | $3.20 |
| Large standard, 12 oz or less | $7.43 | $5.48 | $4.60 | $3.96 |
| Large standard, 16 oz or less | $8.89 | $6.47 | $5.03 | $4.33 |
| Large standard, 1+ to 2 lb | $10.33 | $7.05 | $5.98 | $5.19 |
| Large standard, 2+ to 3 lb | $11.45 | $7.96 | $6.47 | $5.80 |
Payment processing: Amazon Pay's 2.4% plus $0.30 does not apply to merchants using the Shopify app; Shopify may charge its own payment fees instead. Storage follows FBA rates, which rise from October to January. In an integrated cart, Amazon prices the fulfillment fee on all units it ships in the order, so one Prime unit plus one MCF unit is priced as a two-unit order.
Worked example (illustrative): a brand ships 5,000 to 25,000 Shopify orders a month, and 15% of them use Buy with Prime. The average Prime order is one large standard unit of 8 to 12 oz with a $50 order value. Per order, Amazon charges $1.50 (3% service fee) plus $7.43 (fulfillment), or $8.93 before Shopify payment fees and FBA storage.
| Shopify orders a month | Buy with Prime orders (15%, example) | Prime service fees | Fulfillment fees (peak rate card) | Amazon fees before storage |
|---|---|---|---|---|
| 5,000 | 750 | $1,125 | $5,573 | $6,698 |
| 10,000 | 1,500 | $2,250 | $11,145 | $13,395 |
| 25,000 | 3,750 | $5,625 | $27,863 | $33,488 |
Compare the $8.93 with what your 3PL charges for the same order, including pick, pack, packaging and postage, and with the sales lift you measure on Prime-enabled products. For the full fee comparison between MCF and a 3PL, including the fuel surcharge and Preferred Pricing, see Amazon MCF vs a 3PL for Shopify orders.
How do you split inventory between a 3PL and FBA for Buy with Prime?
Enable Prime on a short list of SKUs, size their FBA stock for Amazon.com plus Buy with Prime demand, and keep everything else at the 3PL. The 3PL's stock serves non-Prime orders and is the reserve you send into FBA.
| Example SKU (illustrative) | Daily units, Amazon.com | Daily units, Buy with Prime | Daily units, other Shopify orders | Stock to hold in FBA (35 days of cover) | Stock to hold at the 3PL (21 days of cover) |
|---|---|---|---|---|---|
| Hero SKU, Prime enabled | 40 | 15 | 25 | 1,925 | 525 plus FBA replenishment reserve |
| Second SKU, Prime enabled | 10 | 5 | 15 | 525 | 315 plus FBA replenishment reserve |
| Bundle or kit, not Prime enabled | 0 | 0 | 30 | 0 | 630 |
Days of cover are example targets; set yours from your FBA inbound lead time and safety stock (see reorder points and safety stock). Three Amazon rules affect the numbers:
- Shared demand: Buy with Prime sales draw down the same FBA units as Amazon.com, so a Shopify promotion on a Prime SKU can stock it out on Amazon.
- Low-inventory-level fee: Amazon's low-inventory-level fee page counts units shipped through Multi-Channel Fulfillment in average daily shipped units. Buy with Prime volume therefore raises the stock an FNSKU needs to stay at or above 28 days of supply.
- Capacity limits: Prime stock sits in FBA and uses your FBA capacity. Our guide to FBA capacity limits covers how to plan around them.
Products that do not suit Prime, such as kits assembled to order or items in branded packaging that must ship in your own box, stay at the 3PL. For running Shopify orders and FBA replenishment from one building, see Shopify and Amazon from one warehouse.
Do you need Buy with Prime, or MCF Prime delivery?
Not always. Amazon's MCF app now offers a Prime delivery option inside your normal Shopify checkout, while Buy with Prime adds Amazon sign-in and the Prime-branded checkout.
Per the Buy with Prime FAQ, Prime delivery through MCF shows the Prime badge on products with FBA inventory and lets shoppers pick Prime delivery at checkout without logging in to Amazon. Amazon verifies membership after the order; non-members get complimentary Prime delivery once, then MCF Standard. Prime delivery is available only for orders from your own website, not TikTok or Walmart. Both options ship from FBA, so the inventory split and the double-fulfillment rules above apply either way.
What should you ask your 3PL before turning on Buy with Prime?
- Does your Shopify integration read assigned locations on fulfillment orders and skip items assigned to "Buy with Prime" or "Amazon Fulfillment"?
- Is permitsSKUsharing set to true for your fulfillment service?
- What happens to the non-Prime items in a mixed cart, and do they ship as a separate fulfillment with their own tracking?
- Can you prep and ship replenishment into FBA for Prime SKUs, and how is freight into Amazon billed?
- How will the inventory split show in your reporting, so Shopify stock and FBA stock are not counted twice?
Where does Orderfy fit?
Orderfy is a tech-enabled, modern 3PL for high-volume Shopify and Amazon brands, built Shopify first. It runs Shopify fulfillment and Amazon FBA prep from one warehouse in the center of the US, in Dallas-Fort Worth, so ground shipping reaches both coasts quickly and FBA replenishment ships from the same building.
- Shopify app: natively integrated with Shopify, with real-time inventory sync, tracking sent to Shopify as soon as a label is created, and split shipments supported.
- Orderfy WMS: the proprietary inventory software we built in-house for Shopify and Amazon sellers, included for clients, so you manage your whole inventory in one place. It tracks every order at every stage and follows FBA prep from arrival at the warehouse to sellable at Amazon. Many 3PLs license their WMS from a software vendor. Orderfy built its own.
- Amazon side: Orderfy Prep weighs and measures every outbound carton and keeps box contents accurate, with lower-cost consolidated freight into Amazon and many Amazon fulfillment centers nearby.
- Accuracy and service: Orderfy tracks a 99.9% order accuracy rate in Orderfy WMS, keeps photo records of shipments, and gives clients direct communication channels for 24/7 access to the warehouse team.
For Buy with Prime specifically, ask Orderfy to confirm how its Shopify app treats line items assigned to the Buy with Prime location. Orderfy is not the right fit for brands that want every Shopify order fulfilled by Amazon, for very low order volume where MCF alone is simpler, or for brands that need warehouses on both coasts for 1-day ground delivery.
Frequently asked questions
Buy with Prime is an Amazon program that lets Prime members check out on your own website with their Amazon account and get Prime delivery and free returns on eligible items. Amazon fulfills those items from your FBA inventory through Multi-Channel Fulfillment.
No. You need an active Professional Seller Central account with FBA set up and inventory in Amazon fulfillment centers, but you do not need to list products for sale on Amazon.com. Amazon suggests setting a far-future start selling date to keep a product off Amazon.com.
No. Prime items in a Buy with Prime order are fulfilled automatically by Amazon from FBA stock. Your 3PL ships the non-Prime items in the same cart, and its integration must skip the Prime items to avoid shipping them twice.
The app is free to install. As of October 2026, Amazon charges a 3% Prime service fee (minimum $0.30 per order) plus a per-unit fulfillment fee, such as $7.43 for a single large standard unit up to 12 oz on the peak rate card effective October 15, 2026. FBA storage and Shopify payment fees are separate.
Yes, if split shipping is turned on in Shopify. The Prime items ship from Amazon and the other items ship from your own fulfillment location, so the customer may receive two packages.
Yes. Amazon builds the MCF and Buy with Prime app for Shopify, which syncs catalog, orders, tracking and returns into the Shopify admin. Shopify's help center documents the requirements and setup.
Buy with Prime automates the refund when a shopper returns an item within the free return window. Confirm in the Buy with Prime merchant console where returned Prime units go before you plan on them coming back to your 3PL.
Get a quote
If you are adding Buy with Prime and want one partner for Shopify orders and FBA replenishment, get a quote and include your monthly Shopify orders, the SKUs you plan to enable for Prime, and your Amazon volume.
Sources
- Buy with Prime: Pricing (2026 peak rate card, effective October 15, 2026), checked October 30, 2026
- Buy with Prime: Third-party order management system integrations, checked October 30, 2026
- Buy with Prime: FAQ library, checked October 30, 2026
- Shopify Help Center: Activating Buy with Prime on Shopify, checked October 30, 2026
- Shopify Help Center: Multi-Channel Fulfillment by Amazon, checked October 30, 2026
- Shopify App Store: Amazon MCF and Buy with Prime, checked October 30, 2026
- Amazon Seller Central: Low-inventory-level fee, checked October 30, 2026