Yes, you can sell on Amazon and Shopify at the same time, and plenty of stores do. Amazon becomes a second sales channel, and the hard part is not permission but stock. If both channels draw on the same units and nothing keeps the counts in step, you will sell something you no longer have. The two official tools for avoiding that are Shopify Marketplace Connect, which links your Amazon listings to your Shopify products and syncs orders and inventory, and Amazon Multi-Channel Fulfillment (MCF), which lets Amazon ship your Shopify orders from the same stock it holds for Fulfillment by Amazon (FBA).
This guide explains the three ways to run both channels, what each official tool does and costs, and where overselling still slips through. Everything below was checked against Shopify and Amazon pages on November 2, 2026.
1. Separate stock per channel Your shelf for Shopify, Amazon warehouses for Amazon Amazon (FBA) You Cash tied up in two piles; one runs out while the other sits
2. One shared pool you ship (FBM) Your shelf or warehouse You You Overselling if the sync or your counts are wrong
3. One shared pool at Amazon (FBA plus MCF) Amazon warehouses Amazon (FBA) Amazon (MCF) Per-order MCF fees and less control over packaging and timing
The three common ways to run Amazon and Shopify together. Built from Shopify Marketplace Connect Help and Amazon’s MCF pages, checked November 2, 2026.Is it allowed to sell the same product on both?
Nothing in Shopify’s or Amazon’s tools stops you. Shopify built Marketplace Connect for exactly this, and says you can connect your store to Amazon, eBay, Walmart (United States only) and Target Plus (United States only). Amazon describes MCF as a way to fulfill orders “across all your sales channels” and says it supports “orders placed on any third-party channel: DTC sites, other marketplaces, and social platforms.”
Amazon does have its own seller policies on pricing and on how you contact Amazon buyers. Those Seller Central help pages only load in a logged-in browser, so we could not check their current wording for this article. Read the pricing and buyer communication policies in your own Seller Central account before you set prices across both channels or add inserts to Amazon parcels.
How Shopify Marketplace Connect links the two channels
Marketplace Connect is Shopify’s own app for selling on marketplaces from your Shopify admin. Shopify says “Changes made to products and orders in your online store are automatically synced across your marketplaces.” For Amazon, it does three jobs.
It links listings to your products
If you already sell on Amazon, you link those listings to existing Shopify products. Shopify says the app “searches your Shopify store to suggest a product match based on the product SKU, UPC (Universal Product Code), or title,” and if it cannot find one you pick the match yourself from a drop-down menu. Shopify adds: “After you link your marketplaces listings to your products, Marketplace Connect begins syncing orders and inventory for your linked listings.” Clean, matching SKUs make this step much easier.
It imports Amazon orders into Shopify
You can import Amazon orders automatically or one at a time. Shopify says an imported order “displays in the Orders section of your Shopify admin as though it was placed through your online store,” with the marketplace name shown in the Channel field. You choose whether orders import when they are placed (Pending) or only after the customer has paid in full (Complete). Once you fulfill an order, Shopify says Marketplace Connect “automatically syncs shipping status and tracking updates” back to Amazon.
It handles FBM, FBA and MCF differently
Shopify says that with Amazon connected, you can fulfill orders through Shopify (FBM), Fulfillment by Amazon (FBA) or Multi-channel Fulfillment (MCF), chosen per product.
- FBM: “Marketplace Connect sends the order for those products to Shopify to be fulfilled. Inventory counts are updated in Shopify and on Amazon, and tracking information is automatically sent to Amazon.”
- FBA: Amazon ships from its warehouses. Shopify says you can set up orders to be fulfilled by Amazon automatically, “and after a product’s inventory is depleted from FBA, it automatically switches to your FBM inventory.” That fallback is useful, but it means your own shelf stock can start selling on Amazon once FBA runs dry.
- MCF: to send Shopify orders to Amazon’s warehouses, you turn on the MCF setting inside Marketplace Connect (steps below).
Two limits are worth knowing before you start. Shopify says Amazon, Walmart, eBay and Target Plus require a unique product identifier such as a GTIN, UPC, MPN or EAN for each product, and private label sellers without one need to apply to the marketplace for an exemption. Shopify also says “It’s important to have only one marketplace connector app connected to avoid data conflicts.” Running Marketplace Connect alongside another Amazon sync app is a common way to get stock counts that fight each other.
Shopify’s pages we read do not state how often inventory syncs or offer a documented stock buffer setting, so do not assume updates are instant. If you sell fast-moving items with very low stock, plan for a short delay between a sale on one channel and the count changing on the other.
What Marketplace Connect costs
The app is free to install. Shopify’s App Store listing gives the pricing as “First 50 marketplace-synced orders/mo free, 1% fee per additional synced-order, capped at $99/month,” billed in US dollars. Shopify’s pricing page shows the same terms on every plan: 50 synced marketplace orders a month free, then “1% up to $99/mo.” Manually imported orders are free and unlimited.
Neither page we checked says exactly what the 1% is charged on. Our model below assumes it is 1% of each synced order’s value, which is the most natural reading. Check the charge on your first Shopify bill after you pass 50 orders.
40 $1,400 $0.00 0.00%
150 $5,250 $35.00 0.67%
250 $8,750 $70.00 0.80%
400 $14,000 $99.00 (cap) 0.71%
1,000 $35,000 $99.00 (cap) 0.28%
Hypothetical store with a $35 average Amazon order. Assumes 1% of order value on each synced order after the first 50, capped at $99 USD a month, per Shopify’s App Store and pricing pages checked November 2, 2026. Calculated twice in Python (decimal arithmetic, then a float cross-check).The cap kicks in once the orders after the first 50 add up to $9,900 in value. At a $35 average order, that happens on the 333rd synced order of the month. At a $50 average it happens at 248 orders, and at $25 it takes 446. Below 50 orders a month, the sync is free. These are small numbers next to Amazon’s own selling fees, which we break down in what Shopify, Amazon and Etsy each keep from a $40 sale.
Shipping Shopify orders from your FBA stock with MCF
If your stock already sits in Amazon’s warehouses for FBA, MCF lets Amazon ship your Shopify orders from that same pool. Amazon says it uses “a single pool of inventory” across channels and that it packs orders “with unbranded packaging by default.” Amazon lists two speeds on its MCF page: Standard, which “Delivers to customers in 3 business days,” and Expedited, which delivers in 2 business days.
Amazon publishes an official Shopify app called Amazon MCF and Buy with Prime. It is free to install and Amazon says it lets you “fulfill your orders using Amazon Multichannel Fulfillment (MCF) with the same pool of inventory used for FBA.” The listing says you can place orders to the US, UK, EU, Japan, Canada and Australia, while Prime delivery on your own site and MCF Preferred Pricing are marked US only. If you already use Marketplace Connect, Shopify’s own MCF setting inside that app is the other route. Pick one, given Shopify’s warning about running more than one connector.
What MCF costs during the 2026 holiday peak
Amazon’s MCF rate card shows peak fees “Effective October 15, 2026-January 14, 2027,” and Amazon says “A 3.5% fuel and logistics-related surcharge applies to MCF fulfillment fees in the US.” Here are the single-unit, standard-speed fees for small items, with the surcharge added.
Small standard, up to 4 oz $7.53 $7.79
Small standard, over 4 oz to 8 oz $7.71 $7.98
Small standard, over 8 oz to 12 oz $8.38 $8.67
Small standard, over 12 oz to 16 oz $8.88 $9.19
Large standard, up to 4 oz $7.80 $8.07
Large standard, over 4 oz to 8 oz $7.98 $8.26
Fees from Amazon’s US MCF rate card (peak period October 15, 2026 to January 14, 2027), checked November 2, 2026. Surcharge column is our calculation (fee x 1.035, rounded to the cent) and ignores discounts, lithium battery fees and remote-area surcharges.A few details change the real number. Amazon says fees fall for multi-unit orders (“Save up to 50% on per-unit fulfillment fees when you ship multi-unit orders”), but the rate card’s table headers do not say whether those columns are per unit or per order, so we have only modelled one-unit orders here. Amazon also offers 25% off MCF fees on your first 100 units through its New Seller Incentive, and up to 15% off through MCF Preferred Pricing for eligible US sellers. Orders to Alaska, Hawaii, Guam, Puerto Rico and the Virgin Islands carry a remote-area surcharge of 100% for standard-size items.
Compare these figures with what you pay to pick, pack and ship a Shopify order yourself. If your own cost is close, MCF mostly buys you time. If you are already sending everything to FBA, it saves you keeping a second pile of stock at home. For the Amazon side of that decision, see whether FBA or FBM costs less for your product.
Where overselling still happens
A connector reduces overselling. It does not remove it. These are the gaps we found in the official documentation.
- Cancelled and returned orders are not restocked automatically. Shopify says that in Marketplace Connect, “After an order is returned or canceled, the inventory for the products in the order isn’t restocked.” That avoids overselling, but you have to add the units back yourself or they sit unsold.
- “Continue selling when out of stock” is turned on. Shopify says that by default customers cannot buy a tracked item at zero stock. If someone ticked Continue selling when out of stock on a product, Shopify will keep selling it below zero no matter how carefully Amazon orders sync.
- Inventory is not tracked at all. That option only works when Inventory tracked is on, and an untracked product has no count to sync.
- FBA quietly falls back to your shelf. Once FBA stock runs out, Marketplace Connect can switch the product to your FBM inventory. If that shelf stock is also meant for Shopify, both channels are now selling the same units.
- Two sync apps. A second connector or an old inventory app can overwrite counts. Shopify recommends only one.
- Stranded stock at Amazon. Shopify notes that FBA inventory without an active Amazon offer is “stranded inventory” and “can’t be sold.” It still counts as stock you own, so your totals can look healthier than what is actually sellable.
For very low stock items, a simple habit helps: hold back one or two units from one channel when stock gets low, so a short sync delay cannot cause a cancelled order. That is our suggestion, not a Shopify setting. An oversold Amazon order means a cancellation and an unhappy customer on a channel where you have less control over the relationship. If you are outgrowing a single connector, our guide on how to choose inventory software covers when a dedicated system makes sense.
How to set it up, step by step
Shopify lists these requirements: a verified Amazon seller account in the country you want to sell in, a Shopify online store that is not in private mode, an active payment provider, and shipping rates for the countries you sell to. You also need to display your shipping rates and store policies on the marketplace.
- Clean your SKUs first. Make sure each Shopify variant has a unique SKU and, where you have one, a UPC or GTIN that matches the Amazon listing.
- Turn on inventory tracking for every product you will sell on Amazon, and check that Continue selling when out of stock is off unless you mean it.
- Install Marketplace Connect from the Shopify App Store and connect your Amazon seller account for the right country.
- Link existing listings. Review each suggested match (Shopify labels them “Ready to list”, “Close match” or “No match”) and confirm or fix it.
- Set the inventory location for each product, in bulk or for a whole regional marketplace. Shopify notes you cannot set it for individual variants.
- Choose order import settings: automatic or manual, Pending or Complete, and which fulfillment methods to import.
- If Amazon will ship Shopify orders, go to Apps > Marketplace Connect > Settings > Accounts, select your Amazon marketplace, and in the Amazon Multi-Channel Fulfillment section tick the box to add the “Amazon MCF by Shopify Marketplace Connect” fulfillment service, then save. (Path checked November 2, 2026.)
- Test with one product. Place a small order on each channel and confirm the count drops on the other side before you link the rest of the catalog.
Once orders are flowing, automations can take care of the follow-up, such as tagging Amazon orders or alerting you when stock gets low. Our list of Shopify Flow automations worth setting up first is a good place to start.
Common mistakes
- Linking listings by title alone. Similar titles across variants lead to the wrong product being matched and the wrong count dropping.
- Forgetting to restock returns. Returned and cancelled marketplace orders do not go back into stock on their own.
- Keeping an old sync app installed. Two apps writing stock counts is a recipe for mismatches.
- Treating MCF peak fees as year-round prices. The rates above apply from October 15, 2026 to January 14, 2027.
- Assuming the 1% fee applies from the first order. The first 50 synced orders each month are free.
What you should check next
- List the products you plan to sell on both channels and confirm each has a unique SKU and a product identifier.
- Count last month’s Amazon orders to see whether you would pay the Marketplace Connect fee at all, and roughly how much.
- Price one typical Shopify order through MCF and compare it with your own pick, pack and ship cost.
- Decide who ships what: separate stock, one pool you ship, or one pool at Amazon.
- If you are still deciding where to launch first, read Amazon vs Shopify: where should a new brand start.
Frequently asked questions
Do I need a Professional Amazon seller account to use Marketplace Connect?
Shopify’s requirements page asks for a verified Amazon seller account in the right country and approval to sell, but the pages we read do not name a specific selling plan. The plan choice matters for Amazon’s own fees, which we compare in Amazon Individual vs Professional plan.
Will Amazon orders show up in my Shopify reports?
Imported orders appear in your Shopify Orders list as though placed through your store, with Amazon shown in the Channel field, so you can filter and fulfill them in one place.
Does MCF put Amazon branding on my Shopify orders?
Amazon says MCF uses unbranded packaging by default.
Can I sell on Amazon.ca and Shopify together from Canada?
Yes. Shopify says you can sell “in any region, and in any currency available on your chosen marketplace,” and that you should sign up for an Amazon seller account in the country you want to sell in. Walmart and Target Plus connections are US only.
Can I still connect Etsy through Marketplace Connect?
Not as a new connection. Shopify says new Etsy connections cannot be made at this time, although existing Etsy connections keep working.
The takeaway
Selling on Amazon and Shopify together is normal and supported by both companies. Decide first where your stock lives, then use one connector to keep counts in step: Marketplace Connect for linking listings and syncing orders, and MCF if you want Amazon to ship your Shopify orders too. Most overselling comes from settings around the sync, so check tracking, restocking and duplicate apps before you blame the connector.
Sources
- Shopify Help Center, Shopify Marketplace Connect overview. help.shopify.com
- Shopify Help Center, Marketplace Connect requirements. help.shopify.com
- Shopify Help Center, Marketplace Connect setup and fees. help.shopify.com
- Shopify Help Center, Marketplace Connect: linking existing listings. help.shopify.com
- Shopify Help Center, Marketplace Connect product requirements. help.shopify.com
- Shopify Help Center, Marketplace Connect inventory location. help.shopify.com
- Shopify Help Center, Marketplace Connect order management and order import settings. help.shopify.com, help.shopify.com
- Shopify Help Center, Marketplace Connect order fulfillment (FBM, FBA and MCF). help.shopify.com
- Shopify Help Center, selling when out of stock. help.shopify.com
- Shopify App Store, “Shopify Marketplace Connect” listing and pricing. apps.shopify.com
- Shopify, Pricing page (marketplace order rows). shopify.com
- Amazon Supply Chain, Multi-Channel Fulfillment overview. supplychain.amazon.com
- Amazon Supply Chain, MCF pricing and FAQ. supplychain.amazon.com
- Amazon Supply Chain, MCF rate card, peak fees effective October 15, 2026 to January 14, 2027. supplychain.amazon.com
- Shopify App Store, “Amazon MCF and Buy with Prime” (developer: Amazon). apps.shopify.com
Last reviewed: November 2, 2026. Fees, settings paths and app features were checked on this date; MCF fees shown are the US holiday peak rates in effect until January 14, 2027.
How this article was made: researched and drafted with AI assistance, with every factual claim checked against the sources above. The Marketplace Connect fee table and chart are modelled for a hypothetical store with a $35 average order and assume the 1% is charged on order value; the surcharge column in the MCF table is our calculation and ignores discounts.
Related guides
- Amazon vs Shopify: where should a new brand start?
- Amazon FBA vs FBM: which costs less for your product?
- Shopify vs Amazon vs Etsy fees on a $40 sale
- How to choose inventory software