Business Payments: Reconcile your PayPal and Stripe transactions in QuickBooks


How to your PayPal and Stripe transactions in QuickBooks

This guide will give you a clear picture of what needs to happen in QuickBooks Online after you have synced your transactions using .
  • In this guide we will discuss the best way our customers have found to reconcile and match online payments in QuickBooks.
  • In a nutshell, we are going to replicate the money flow that takes place when you first receive money into your Online Payment system, and then transfer it to your bank.
  • Before you start preparing your , make sure you do not have any other PayPal or Stripe apps connected to QuickBooks as this could lead to duplicates.


  1. Sync
  2. Transfer
  3. Reconcile

Step 1

Sync online sales and expenses via Business Payments into a specifically set up buffer account “PayPal” or “Stripe”. If you don’t have such an account, our app will auto-create it during the initial setup.
By syncing your transactions into the buffer account, you will have the starting point to then transfer the amounts into your bank from, thus reflecting the actual money-flow.


*We recommend to use a buffer account and not your actual bank account, because bank account will not include the fees you pay to PayPal and Stripe, therefore your balance will be off by the amount of fees you paid.
Find out more about recommended buffer accounts in this article.

Step 2

After the synchronization is done, make sure your Bank account in QuickBooks Banking is up to date. If you are using Stripe, most likely it deposits the funds into your bank automatically once a day. If you are a PayPal user make sure to withdraw the amounts that you have synced with Business Payments into your actual bank in order to proceed.
Once you have synced your transactions into a buffer account, you can go to Banking section in QuickBooks and open transactions that are currently For Review.
Once you have pulled in the recent online transactions into your bank account, select each of them and click on Transfer to and run a transfer of the corresponding amount from the buffer account into your current bank account.
If you had 10 transactions in one day, $100 each and received an automatic deposit of $1000 from Stripe into your actual bank, you can transfer a $1000 from your Stripe buffer account into your Bank account, thus balancing out the QuickBooks Balance with Bank balance.
Your aim would be to reach equal amount on both: your Bank balance and QuickBooks balance.

Step 3

When you are all set in Banking, you can reconcile the buffer account in your Chart of Accounts to match the transactions on your monthly bank statement with the transactions you entered into QuickBooks Online.
To reconcile an account in QuickBooks Online, click the Gear button. Then click the “Reconcile” link under the “Tools” heading in the drop-down menu to open the “Reconcile” page.
Use the “Account” drop-down as pictured on the screenshot to select PayPal/Stripe bank. Enter the ending balance of the bank statement into the “Ending balance” field. Then enter the statement’s ending date into the “Ending date” field.
        If needed, enter any bank service fees or interest earned into the “Enter service charges and interest earned, if any” section. Enter any PayPal/Stripe service fees into the “Service charge” field and then select the date and the account used to track bank service fees from the adjacent “Date” and “Expense account” drop-downs.
Click on Start reconciling
  1. In the “Reconcile (Account name)” window that opens, the account transactions appear on the “Payments,” “Deposits,” and “All” tabs.
  2. To mark transactions as “cleared,” click the small circles at the right end of the transaction rows.
  3. The information that was synchronized from the account statement appears at the top of the window.
  4. To change the information from the account statement, click the “Edit info” button in the upper-right corner of this window to open an “Edit the information from your statement” panel at the right side of the window. Save all changes or cancel.
  5. To finish after successfully reconciling an account, click “Finish now” to save it.
  6. To save your work and finish reconciling later or to leave to investigate an account discrepancy, select the “Save for later” option to save your work.
  7. After you successfully reconcile an account in QuickBooks Online, a reconciliation report becomes available.
  8. To view the report in the “Success! You reconciled your account.” window that appears, click the “View report” button.
  9. Otherwise, click the “Done” button in this window to close it.
  10. To view your Reconciliation statement later, click on “Reconcile” under “Tools” heading in the drop-down menu to open the initial “Reconcile” window again and click on “Reconciliation history” in the upper-right corner of that window. The account’s previous reconciliation reports then appear in list below. To open the report for the desired period, click the “View report” link under the “Action” column. To print it, if needed, click the “Print” button in the upper-right corner of the report.
Ideally, we are looking for a $0 difference, which will balance your QuickBooks balance with your bank statement. We recommend to repeat this process regularly, which will be accessible thanks to Business Payments.
Congratulations! You are all set.
By syncing into a buffer account using the flow recommended in this guide, all of your online Sales and Expenses will be matched with your current bank account.
Bank balance and QuickBooks balance will be even and you will be able to easily keep track of your online Sales and Expenses.

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