Shopify and Amazon from one warehouse: how a hybrid setup works

What are the ways to run Shopify and Amazon together?

There are three common setups. Google's AI Overview for this query points mainly to the first.

Shopify's help page also says you do not need to sell on Amazon to use MCF, and that MCF is pay-as-you-go. If most of your volume is Shopify and you want control of packaging, inserts and carrier choice, a 3PL usually gives you more of that than MCF does. Compare real rates for your SKUs, not headline ones: see what a 3PL costs per order.

How does one inventory serve two channels?

Think of the stock in the building as three buckets: available for Shopify, reserved for FBA replenishment, and in transit to Amazon. A unit only changes bucket when someone moves it.

• Shopify bucket: pick-and-pack inventory in bins. This is what the store shows as available.
• FBA reserve: units pulled for the next Amazon shipment. They are no longer sellable on Shopify, so the available count must drop when they are pulled.
• In transit or at Amazon: inventory Amazon owns the sale of until it sells or is removed.

The count is the hard part. If your 3PL's system does not subtract FBA pulls from the Shopify quantity, you oversell on the store. Ask exactly how it works before you sign, and how often the count updates.

What does a hybrid month look like? A worked example

Illustrative numbers, not a client result. A brand sells 12,000 Shopify orders a month with 1.5 units each (18,000 units) and 6,000 units a month on Amazon through FBA.

At 200 units a day on Amazon, 14 days of cover is 2,800 units. Say you want to keep about three weeks at FBA to absorb a 7-day lead time and some variance: 21 days x 200 = 4,200 units on hand at Amazon. Replenishing in two 3,000-unit shipments a month keeps FBA near that level without storing excess in Amazon's fees. In a two-inventory setup you would typically carry that safety stock at both places; in the hybrid, only the Amazon portion sits at Amazon and the rest remains sellable on Shopify.

The point of the example is the cadence: smaller, more frequent FBA shipments from a pool you control, instead of one large annual send-in. If you run up to peak, see the peak season planning guide.

Who preps the units for Amazon?

Amazon ended its US prep and labeling services on January 1, 2026, so units you send to FBA must arrive prepped by you or your warehouse (Amazon FBA prep and the end of de minimis). In a hybrid, this is the key capability to check: your Shopify units can ship in your branded packaging, while FBA units need an FNSKU label, any bagging and set labeling required by Amazon, and cartons that meet its limits.

• Unit prep and barcode rules: our FBA prep mistakes checklist.
• Carton size, weight and labels: Amazon's own carton requirements.
• A practical rule: label for FBA at the time of pull, not at receiving. A unit with an FNSKU sticker and the manufacturer barcode covered cannot go back to Shopify without relabeling, so apply FNSKUs only to units assigned to a shipment.

How should you send inventory to Amazon: parcel or freight?

Small parcel works for small replenishments; LTL or full truckload is better as shipments grow. Consolidated full truckload typically costs far less per unit than small parcel for inventory going into Amazon. Ask for example per-carton or per-pallet freight rates to the Amazon destinations you use.

Freight is billed separately from prep at Orderfy. When you compare 3PLs, ask whether the quote includes freight to Amazon and who books the carrier and the dock appointment.

What should you ask a 3PL before you run both channels?

1. Can you prep to Amazon rules in-house (FNSKU labels, bagging, set labeling) and do you list the prices per unit?
2. How is the Shopify available quantity updated when units are reserved for FBA?
3. What is your cutoff for same-day Shopify shipping?
4. Can you build FBA cartons to Amazon's size and weight limits and upload box contents?
5. Do I get photos of each inbound and outbound shipment and a direct line to the team?
6. How do you handle an Amazon removal order coming back?
7. What is my total cost per unit for Shopify orders and for FBA units, itemized?

Where Orderfy fits

Orderfy runs both sides from one building in Garland, Texas, in the Dallas-Fort Worth area, in the center of the US. Shopify orders ship same day. Orderfy Prep handles the Amazon side with Orderfy WMS, our proprietary inventory software built in-house, and consolidated freight to Amazon. Clients get photo records of each shipment and direct communication channels for 24/7 access to the warehouse team. Being in the center of the US helps ground shipping reach both coasts quickly. Inventory syncs to Shopify in real time, the client portal tracks Amazon FBA prep from arrival at the warehouse to sellable on Amazon, and prep orders are typically ready to ship to Amazon the same day.

Shopify orders and Amazon FBA prep run from one inventory in Orderfy WMS, a proprietary WMS built in-house, so the Shopify count and the FBA count come from the same stock.

Orderfy is not the right fit if you are under a few hundred orders a month, if you want Amazon to fulfill and ship everything through MCF, or if nearly all your customers sit on one coast far from Texas.

Frequently asked questions

Sources

• Multi-Channel Fulfillment by Amazon, Shopify Help Center, read October 2026
• Orderfy: pricing and services, llms.txt
• Amazon US prep services ending January 1, 2026: Orderfy guide