1. Synder setup 
  2. Sync your payments and Payouts
  3. QuickBooks Flow 

Our customers have found that the most accurate way to record all PayPal sales, fees, expenses, and refunds is to sync everything into a “clearing” account in QuickBooks Chart of Accounts. The app will create a “PayPal Bank Account” and once your PayPal withdraws money to your Bank the app will record transfer from PayPal Bank Account to your Checking, therefore replicating the actual money-flow when funds first hit your PayPal account and then are transferred to bank checking. 

*Before you begin, make sure you currently don’t have PayPal connected in QuickBooks banking nor use any other synchronization apps, as this could lead to duplications

Step 1

Make sure you have the clearing (PayPal Bank Account) account selected as a Bank account in Sales and Fees and Expenses tabs. 

Make sure the Payouts are enabled in Synder settings and your Checking account is selected there.

Step 2

 Sync PayPal transactions and payouts manually or set up an auto-sync for ongoing transactions.

 Step 3

 Open For Review list in QuickBooks Banking tab and match your PayPal automatic withdrawal with transfers (payouts) created by the app. Click on Match near every PayPal line.

Congratulations! You have successfully pulled in all PayPal data and can easily reconcile your checking account now avoiding manual data entry and having recorded all sales, fees, expenses, and refunds. 


  • The PayPal Bank Account balance should be equal to the balance of your actual PayPal (or very close to it in case some transactions are still in the process of the sync), this way you can track that everything works properly. 
  • If you would like to reconcile PayPal Bank Account you can use the PayPal reports for this.
  • PayPal Bank Account will not show up under the Banking tab in QuickBooks, this is the correct flow of the app, so no worries. 

Should you have any questions, please contact us via online support chat, phone, or email.


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  1. Bronte Austin

    What about transactions that are paid for by check? These are technically not deposited into my Paypal account online. Will this same method work?

    1. Fanya

      Hello Bronte, thank you for your question! If I understood you correctly, you refer to check payments into your checking account.
      You can use another application of ours, Business Importer (, to create check records in your checking account in QuickBooks Online. You can import a spreadsheet with info for all the checks that need to be created, saving time on manually entering each check (read how to do it here:
      Once the checks are in QuickBooks, you can open “For Review” of your checking account and click on match next to each transaction in your checking that is already recorded in QuickBooks.

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