How to Reconcile PayPal transactions in QuickBooks Online: Quick Guide

Reconcile PayPal transactions in QuickBooks

How to Reconcile PayPal transactions in QuickBooks Online: Quick Guide

  1. Synder setup
  2. Syncing Transactions
  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 Bank account in QuickBooks Chart of Accounts and then run a 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 checking.
*Before you begin, make sure you currently don’t have PayPal connected in QuickBooks banking nor use any other synchronisation apps, as this could lead to duplications.

Step 1 

In case you don’t have an account with “PayPal” in it, our app will auto-create it. Check your Synder settings to make sure you have that account selected as Bank account in Sales and Fees. If you are using the same checking account for income and expenses, use the same clearing account as Bank account in Expenses.


Step 2 

Sync PayPal transactions manually or set up an auto-sync.

Step 3 

Open For Review list in QuickBooks banking and choose Transfer, selecting your PayPal Banm account from the drop down list. Confirm by clicking on transfer.


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.


This entry has 3 replies

  1. Bronte Austin says:

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

    • Fanya says:

      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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