Ecommerce plugins

Amazon Pay with Shopify Payments

Amazon Pay is working with Shopify Payments to simplify managing your transactions. By doing so, this will offer a familiar checkout experience with improved decline handling. Amazon Pay is currently in the process of making major improvements in the checkout experience with Shopify. We will continue to support merchants that have the existing Amazon Pay checkout version until the new checkout is fully ready. You will now have a consolidated view of any orders that use Amazon Pay within your Shopify admin panel, including Buy with Prime orders when using the Buy with Prime app.

What stays the same between Amazon Pay and Amazon Pay with Shopify Payments

Your customers will still be able to easily and securely speed through checkout on your site using their Amazon account information to access the payment methods and shipping addresses they have on file. If you have enabled the Buy with Prime Shopify app, Prime members will be able to get fast, free shipping and returns on the products they love on your site.

What changes between Amazon Pay and Amazon Pay with Shopify Payments

When you enable Amazon Pay with Shopify Payments you will no longer have to use your Amazon Pay merchant account in Seller Central to manage new transactions and reporting. New orders using Amazon Pay with Shopify Payments will not be displayed in your Amazon Pay merchant account within Seller Central. All transactions, and reporting for Amazon Pay with Shopify Payments will be managed in your Shopify admin panel and will be subject to your Shopify Payments pricing.

How will my Amazon Pay pricing agreement be impacted?

Once Amazon Pay with Shopify Payments is activated, your current Amazon Pay pricing agreement will no longer apply and Amazon Pay transactions will be subject to your Shopify Payments pricing.

Is there an additional fee for Amazon Pay transactions if I activate Amazon Pay with Shopify Payments?

Amazon Pay transactions through Shopify Payments will be subject to your Shopify Payments pricing. There isn’t an additional fee for Amazon Pay transactions on top of your current Shopify Payments pricing.

Is activating Amazon Pay on Shopify Payments a reversible action?

Once you deactivate the direct integration of Amazon Pay on your Shopify store and enable Amazon Pay with Shopify Payments, you will be unable to reverse this change. Your Amazon Pay pricing agreement for the direct integration will no longer apply and Amazon Pay transactions on Shopify Payments will be subject to your Shopify Payments’ pricing.

If you would like to deactivate Amazon Pay in your Shopify Payments Wallet, you can do so by deselecting Amazon Pay in the Wallets Section of the Shopify Payments page within the Shopify admin panel. If you have enabled the Buy with Prime app, de-selecting Amazon Pay in the Wallets Section of the Shopify Payments page will disable Buy with Prime.

Managing your Amazon Pay account after switching to Amazon Pay with Shopify Payments

After enabling Amazon Pay with Shopify Payments, you may still need to access your Amazon Pay merchant account via Seller Central to manage legacy transactions. The following actions will be performed in Seller Central for legacy transactions:

Viewing reporting
Viewing tax document library
Managing Amazon Pay A-to-z Guarantee Claims
Managing Chargeback Claims
Accessing Buyer-Seller Messages

Managing legacy transactions in your Amazon Pay account

When enabling Amazon Pay with Shopify Payments, you will still have to the ability to manage your legacy transactions in your Shopify admin. To do so follow Shopify’s Managing Your Orders help page.

If you decide to manage your legacy transactions directly within your Amazon Pay merchant account or you have switched from another eCommerce Solution Provider and need to manage your prior Amazon Pay transactions, take these steps to manage your transactions within your Amazon Pay merchant account:

Charging transactions:

Sign in to your account on Seller Central.
Click the ☰ menu in the upper left
Click Orders and select Manage Transactions
Enter the Amazon Pay transaction ID starting with “P01” in the search field with Amazon Reference ID as the default search parameter.
- If you only have the customer’s email address, change the search parameter from Amazon Reference ID to “Buyer Email”
Select Search
In the Action column select Collect Payment
Enter the charge amount and an optional note.
Select Review
When ready select Charge

Note: This will charge any existing open authorization. If you do not have an existing open authorization, we will attempt to authorize the customer’s payment instrument and charge the customer. Allow up to 24 hours for the charge status to update.

Refunding transactions:

Sign in to your account on Seller Central.
Select the hamburger menu in the upper left
Click Orders and select Manage Transactions
Enter the Amazon Pay transaction ID starting with “P01” in the search field with Amazon Reference ID as the default search parameter.
- If you only have the customer’s email address, change the search parameter from Amazon Reference ID to “Buyer Email”
Select Search
In the Action column select Refund
Enter the refund and optional refund note. By default, the full refund amount will auto-fill. If you wish to issue a partial refund edit the amount before submitting.
Select Review
When ready select Refund

Note: Confirm the amount you would like to refund before submitting. Amazon Pay is unable to cancel refunds once they’re submitted. Refunds may take up to 7 days to complete.

For more information on managing transactions including our Amazon Pay University video see Manage Transactions

Managing your legacy reports and account balance in your Amazon Pay merchant account

When enabling Amazon Pay with Shopify Payments you may wish to access your reports or view your account balance. For information on how to view reports, and managing your account balance see the sections below:

Reporting and Reconciliation:

Account Balance:

After enabling Amazon Pay with Shopify Payments, you may have a positive or negative balance on your Amazon Pay merchant account.

Positive Account Balances: Your funds will be disbursed in accordance with our reserve policy. However, if your funds have not disbursed be sure to check that you have a valid charge method and deposit method on file. See Accessing funds in Seller Central for additional information. If you have a valid charge method and deposit method on file review your Performance Notifications to ensure you do not have any outstanding requests for information by taking the following steps:

Sign in to your account on Seller Central.
Select the hamburger menu in the upper left
Click Performance and select Performance Notifications
Review any notifications with the subject line: “Your Amazon Pay account” and provide the requested information.

If you have additional questions about remaining funds in your Amazon Pay merchant account balance contact Amazon Pay Merchant Support.

Negative Account Balances: If you switched to Amazon Pay with Shopify Payments, you will not have incoming funds to your Amazon Pay merchant account; refunds, Amazon Pay A-to-z Guarantee Claims, and Chargeback Claims may result in a negative account balance. To recover the negative balance, we will attempt to use the charge method on file. Be sure your charge method is up to date by taking the steps in Accessing funds in Seller Central. You may also repay your balance by taking the following steps or clicking on this link:

Sign in to your account on Seller Central.
Select the hamburger menu in the upper left
Click Reports and select Payments
Select Repay Balance
Select one of the credit cards on file
Select the Outstanding Amount or enter Other Amount
Select Submit Payment

Your Amazon Pay merchant account after migration

After you have successfully switched to Amazon Pay with Shopify Payments, your Amazon Pay merchant account within Seller Central will be used to associate the checkout session with your Amazon Pay account and receive the necessary information to process the payment.

To continue using Amazon Pay with Shopify Payments your Amazon Pay merchant account must remain open and in good standing. Closing your account will disable Amazon Pay in the Shopify Wallet and the Buy with Prime app if enabled. There are no ongoing fees to keep your account open and if you wish to disable Amazon Pay on your Shopify site please do so within the Shopify Payments Wallet.

Further Assistance

If you require further assistance managing your Amazon Pay merchant account within Seller Central, please contact Amazon Pay Merchant Support.

If you have further questions or need assistance with Amazon Pay with Shopify Payments, please contact Shopify Support.

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