How to Sync eBay Transactions into QuickBooks Online using PayTraQer

October 17, 2025

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

Step 1: Open the eBay connector in PayTraQer

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

  • In the left menu, select Connectors.

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

Select Ecommerce Connector - Ebay.png

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

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

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

ebay see how it works.png

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

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

Commerce System 

QuickBooks

Payment

Sales Receipt,  Fees as Expense 

Invoice Payment

Invoice Payment, Sales Receipt,  Fees as Expense 

Customer Refund

Refund

  • Click “OK” once you have reviewed the transaction flow.

ebay user guide.png

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 eBay 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 eBay 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 eBay transactions you want to process.

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

  • Use Sync to upload all selected eBay 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 eBay transactions in one go instead of syncing them one at a time.

Step 4: Start the sync review for an eBay transaction 

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

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

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

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

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

Step 5: Confirm the synchronization result

  • After the sync, check the Synchronization Details window.

  • Make sure the status shows Successful.

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

Step 6: Verify the synced transaction in PayTraQer

  • Go to the Synced tab to check the eBay 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 check the record directly in QuickBooks Online.

Step 7: Review past sync

  • Go to the Sync History tab to look at previous eBay 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 eBay transaction that was synced earlier.

Step 8: Open the eBay Sync Settings page 

Ebay Sync Settings.png

  • In the left menu, select Settings.

  • Choose Sync Settings from the list of options.

  • Find the eBay connector card on the page.

  • Click Change Settings to access the eBay sync configuration.

Ebay Change Settings.png

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

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

Step 10: Configure the Sales tab

Ebay Sales Settings.png

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

  • Under Accounts, choose the Bank Account for depositing your sales or income. This is generally your eBay 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 eBay 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

Ebay Product and Service Settings.png

  • Open the Product & Services tab.

  • Enable the option to automatically create products or services if the eBay 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 eBay 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 eBay items and QuickBooks products or services.

  • If you prefer all eBay 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 eBay items sync properly.

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

Step 12: Configure the Tax tab

Ebay Tax Settings.png

  • Open the Tax tab.

  • Enable automatic tax calculation so PayTraQer computes and applies tax for all eBay 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 eBay tax amounts.

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

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

  • These links assist PayTraQer in posting eBay 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

Ebay 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 eBay Fees.

  • You can pick the bank account where payment fees will be recorded. In the image, the eBay 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.

  • The Fees Category section shows various eBay fee types and allows you to link each one to the appropriate QuickBooks account.

  • Fee types include advertising fees, early termination fees, listing fees, international selling fees, insertion fees, payment dispute fees, subscription fees, promotional fees, reserve price fees, shipping label fees, vehicle listing fees, other fees, and loan repayment fees.

  • Each fee name has a dropdown for accounts next to it, enabling users to assign the right accounting category for precise expense tracking.

  • After reviewing all fee mappings, users can click Save to implement the eBay fee sync settings.

Step 14:  Configure the Payout tab

  • Next, open the Payout tab.

  • Decide if you want to handle payouts or settlements from eBay.

  • Turn on this option if you want PayTraQer to sync payouts as transfer transactions to your chosen checking account.

  • Check the payout settings thoroughly, then click Save.

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