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Reconcile Amazon Pay Transactions in QuickBooks

Learn how to easily reconcile your payments and deposits in QuickBooks with PayTraQer.



Before you get started,You will need to set up PayTraQer and
configure these settings to easily reconcile your account.


  • Connect your QuickBooks and Amazon Pay accounts.
  • Align the Sales, Fees, and Payout settings in PayTraQer, before you start syncing transactions.
  • Choose Amazon Pay Bank Account to deposit your Sales and Fees. This will be your clearing account in QuickBooks.
  • In the Payout settings, enable payout processing and specify the checking account (actual bank account) to transfer your sales.
  • By doing so, all your Amazon Pay sales, fees and other transactions will be posted to the Amazon Pay Bank Account. 


Pro Tip: This clearing account should be used ONLY to record your Amazon Pay sales and transactions.

Match Amazon Pay Transfers

In QuickBooks, you will have to match your Amazon Pay Transfers against your bank deposits before you go for reconciliation. 


  • In the left side panel, navigate to Banking > Banking.

  • You can see the bank feeds of the selected account there. 
  • Your Amazon Pay payouts will be recorded as Transfer in QuickBooks and matched against deposits in the bank feeds. 
  • Choose the transactions and click the Match button. 

If you have not enabled payout processing in PayTraQer, you will have to manually scroll over scattered records to match them on the reconciliation page. 

QuickBooks Reconciliation

  • In QuickBooks, navigate to the Settings iconcog > Reconcile

If you are reconciling for the first time, click Get Started.

  1. In the Accounts dropdown menu, choose the Checking account that you want to reconcile. 
  2. Your beginning balance will appear under the chosen account. 

           Make sure the beginning balance is the same as the one on your bank statement. 

  1. Specify the Ending Balance and Ending Date
  2. Click the Start Reconciling button. 

        You will be directed to the reconciliation page.



 Compare & Match the Statements

  • All your Amazon Pay payments and deposits as recorded in QuickBooks will appear on the screen. 
  • All you have to do is go over each transaction and compare them one by one with the bank statement. 
  • There is a check box to the right of each transaction. Give each transaction a tick when you find it in the bank statement. Leave out the transactions that you do not find in the bank statement.

Transactions that were matched and categorized earlier will be automatically tick-marked here. 


Pro tip: 

  • For easy categorization, you can select Payments or Deposits.
  • Also, you can easily search transactions with the filter option.
  • Repeat the step until you bring down the difference to zero. 

When you complete ticking all the transactions from your bank statement, you should be able to match the accounts with zero difference.

  • With PayTraQer, you will not miss out on any transaction or face any duplicate transaction issues. With proper records, you will be able to get perfectly balanced books, without any friction.

  • When done, click the Finish now button.
  • You will receive a success message.
  • You can view and print your reconciliation report by clicking on the View reconciliation report button.


Related articles - Amazon Pay QuickBooks Integration

  • For more information about How to connect AmazonPay Account with QuickBooks, refer to this article.
  • For more information about how to Obtain Amazon Pay Secret Keys, refer to this article.



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