How to Sync Amazon Transactions into QuickBooks Online using PayTraQer

October 17, 2025

Before you get started

To download and sync Amazon transactions into QuickBooks Online, you must link your Amazon account with PayTraQer. This article explains how to connect your Amazon account with PayTraQer.

Step 1: Open the Amazon connector in PayTraQer

  • Log in to PayTraQer with the QuickBooks Online company you wish to sync with Amazon.

  • In the left menu, select Connectors.

  • Choose e-Commerce Connectors to see the e-Commerce platforms linked to your PayTraQer account.

Select Ecommerce Connector.png

  • Find your Amazon connection in the list before proceeding to the next step.

Step 2: Review how Amazon transactions will be recorded in QuickBooks

  • In the Amazon connector row, click on See How It Works.

Amazon See How it Works in PayTraQer.png

  • A User Guide window will open, showing how PayTraQer syncs Amazon transactions into QuickBooks entries.

  • Under Transaction Recording, check the mapping displayed for your Amazon Sync.

  • Make sure that the payment is recorded as Invoice Payment, and Fees as Expense in QuickBooks.

  • Confirm that Customer Refund is listed as Refund in QuickBooks.

Step 3: Open the Transactions page in PayTraQer 

  • On the left menu, select Transactions.

  • The Transactions dashboard has various organizational views that assist in managing and checking your data flow:

Section

Purpose

Review

Lists transactions that are ready for syncing.

Synced

Includes transactions that have already been sent to QuickBooks.

Error

List transactions that failed and require correction.

Ignore

Keeps track of transactions you deliberately avoided.

Sync History

Provides a full timeline log of previous syncs.

  • Stay in the Review tab to view Amazon transactions that are prepared to sync with QuickBooks Online.

  • In the Review tab, click on Filter.

  • You can use options such as Date, Amount, Payment System, Transaction Type, Transaction ID, and Contact to filter the records.

  • Select Current Page if you want to choose all transactions that are currently displayed.

  • By applying the required filters, you can quickly find the Amazon transactions you need to review or sync.

  • This makes it easier to work with only the relevant transactions instead of going through each record manually.

  • Once you have applied the necessary filters, choose the Amazon transactions you want to process.

  • The selected records will be highlighted, and the total number of selected transactions will be visible at the bottom.

Amazon Review Tab in PayTraQer.png

  • Use Sync to upload all selected Amazon transactions to QuickBooks Online at once.

  • Choose Ignore if you do not wish to sync the selected transactions.

  • Click Clear Selection to discard the selected records and restart if necessary.

  • This option enables you to manage multiple Amazon transactions in one go instead of syncing them one at a time.

Step 4: Start the sync review for an Amazon transaction 

  • To sync the transaction, click on Review & Sync.

Amazon Review and Sync.png

  • PayTraQer will display the transaction details on the right side of the screen.

  • In this section, confirm the Amazon transaction number, date, and amount.

  • Also, check the QuickBooks transaction type that is mapped for this record.

  • Ensure you are looking at the right Amazon payment before proceeding.

Step 5: Confirm the synchronization result

Amazon Right Side review tab.png

  • After the sync, check the Synchronization Details window.

  • Make sure the status shows Successful.

Amazon Successfull in PayTraQer.png

  • Verify the QuickBooks entries created for the transaction, including the Invoice and Payment.

Step 6: Verify the synced transaction in PayTraQer

Amazon Synced Tab in PayTraQer.png

  • Go to the Synced tab to check the Amazon transactions that are already in QuickBooks Online.

  • Select Report if you want to see the sync summary.

  • If the transaction was mistakenly posted, use Undo to reverse the sync from PayTraQer.

  • Use Details to review what was generated for the synced record.

  • Click on Open in QuickBooks, and check the record directly in QuickBooks Online.

Step 7: Review past sync

  • Go to the Sync History tab to look at previous Amazon Sync activities.

  • Look at the sync date, the types of transactions made, and the count of successful or failed records.

  • This page helps you monitor earlier sync operations and verify what was posted.

  • If needed, you can use Undo here to reverse an Amazon transaction that was synced earlier.

Step 8: Open the Amazon Sync Settings page 

Amazon Sync Settings.png

  • In the left menu, select Settings.

  • Choose Sync Settings from the list of options.

  • Find the Amazon connector card on the page.

  • Click Change Settings to access the Amazon Sync configuration.

  • Ensure the Amazon settings screen is displayed before making any changes.

  • This page allows you to manage how Amazon Sales, items, customers, taxes, and fees sync with QuickBooks Online.

Step 10: Configure the Sales tab

Amazon_Sales_Settings_.png

  • Open the Sales tab in the Amazon Sync Settings screen.

  • Under Accounts, choose the Bank Account for depositing your sales or income. This is generally your Amazon clearing bank account.

  • Choose the Payment method to track these transactions in QuickBooks.

  • In the Customers section, decide if PayTraQer should automatically create customers if they don't exist in QuickBooks Online.

  • If you prefer all sales to go to one customer, select a Common Customer for sales transactions.

  • Use “Customize Customer Matching” if you want PayTraQer to match Amazon customers with existing QuickBooks customers based on your chosen matching rule.

  • In the Tracking section, choose the correct Location or Department if you use locations in QuickBooks.

  • Select a Class if you want all synced sales to be assigned to a specific class.

  • In the Sync section, decide if you want to skip the sales and only process the related fees.

  • Click Save after finishing the Sales tab settings.

Step 11: Configure the Product and Services tab

Amazon_Product_and_Services_Settings.png

  • Open the Product & Services tab.

  • Enable the option to automatically create products or services if the Amazon item isn't already in QuickBooks Online.

  • Select the type of product or service that PayTraQer should generate, like Non-Inventory, if it suits your workflow.

  • Pick the income account that will be associated with the products or services created from Amazon transactions.

  • In the Match Product section, decide how product matching should occur, such as by Name.

  • Use Customize Product Matching to establish precise matching rules between Amazon items and QuickBooks products or services.

  • If you prefer all Amazon sales to use a common item in QuickBooks Online, enable the common product or service option and choose that item.

  • Carefully review the product setup to ensure that new and existing Amazon items sync properly.

  • Click “Save” once the Product and Services settings are finalized.

Step 12: Configure the Tax tab

Amazon_Tax_Settings.png

  • Open the Tax tab.

  • Enable automatic tax calculation, so PayTraQer computes and applies tax for all Amazon sales and expenses.

  • The Auto Tax Calculation feature is turned on, allowing PayTraQer to compute and apply taxes for both sales and expenses automatically.

  • The Tax Accounts Mapping area allows you to select the QuickBooks accounts for recording Amazon tax amounts.

  • Sales Tax is linked to the Amazon Sales Tax account.

  • Withheld Tax is also linked to the Amazon Sales Tax account.

  • These links assist PayTraQer in posting Amazon sales tax and withheld tax to the appropriate QuickBooks accounts during synchronization.

  • Users can access Advanced Settings for additional tax configuration options.

  • Click “Save” after you finish with the Tax tab.

Step 14:  Configure the Fees tab

Amazon_Fees_Settings.png

  • The Fees tab in PayTraQer allows you to manage how eBay-related fees are logged in QuickBooks.

  • You can choose the vendor that receives the payment fees. In this case, the vendor is set to eBay.

  • You can select the fee category for recording the expense. Here, the chosen category is Amazon Fees.

  • You can pick the bank account where payment fees will be recorded. In the image, the Amazon Bank Account is chosen.

  • The Auto Tax Calculation section lets you input tax information for fees and select a location or department if necessary.

  • You can choose whether to separate fee details during syncing. The current option is disabled.

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