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 with the help of Paypal QuickBooks Online integration.

*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

First of all, go to Settings to make sure all the accounts are selected correctly. To access settings select the organization needed at the top right of the page – – > Settings button on the left menu of the app – – > find payment platform (if you have several connected) you want to customize settings for – – > click on the Configure button.

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

select clearing PayPal Bank Account as a Bank account in Sales and Fees and Expenses tabs

Make sure to enable the payouts feature in Synder settings and select your Checking account.

check if Payouts are enabled in Synder settings

That’s it!

Step 2

Sync PayPal transactions and payouts automatically with QuickBooks or turn on the manual mode.

NB!: this will work for newly appearing transactions, historical ones are to be synchronized manually, if that is needed. See how to import historical transactions into your accounting platform.

 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.

List in QuickBooks Banking tab

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.

  2. Clara Diaz

    I am trying to reconcile my PayPal and checking accounts for the month of July. There was a transfer made from the checking to the paypal account on June 30th.This transfer shows up in the June statement for the Paypal account and it shows up on July 1st for the checking account. If I try to reconcile the bank account, I need to include the transfer so it matches with the statement but the transfer then will show up in the Paypal account on July 1st and I cant haven’t it July because PayPal recorded it on June 30th. How can I work arounf this?

    1. Polly Sidoruk

      Hello Clara, thank for posting here! If I got you right, the easiest way would just be to find the transfer you are talking about in QuickBooks and change the date so that it matches the date of the bank record (in bank feeds) and then match them.
      Synder records the date that was given by your PayPal, though it can differ from the date when funds hit the bank, however after the transaction was synchronized to your QuickBooks you can easily change any field there, once that is needed.

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