Business Payments: How to Reconcile your Square transactions in QuickBooks Online

Square and QBO Reconciliation

How to Reconcile your Square transactions in QuickBooks Online

This guide will give you a clear picture of what needs to happen in QuickBooks Online after you have synced your transactions using Business Payments.
  • Accountants’ favourite way to reconcile Square payments in QuickBooks.
  • For one-step QuickBooks reconciliation, enable payouts processing in Business Payments settings before you begin with Step 1 to get instant matches of your Square payments and withdrawals to your checking account. Learn more about Payouts here.


  1. Sync
  2. Match
  3. Reconcile ( Standard QBO reconciliation process)

  Step 1

Sync Square transactions into Square Bank Account

*We recommend to sync transactions into a “Square Bank Account” representing your Square and not your actual checking account, because checking account will not include the fees you pay to Square, therefore your balance will be off by the amount of fees you paid. 

Find out more about Business Payments settings and bank accounts here.

Step 2

Step 2: After the synchronization is done, you are able to run a reconciliation in QuickBooks. If you sync manually, you will be able to sync historic transactions up until the most recent ones. In case you have enabled auto-sync, our app will check Square for new transactions every hour. Actual withdrawals from Square that you most likely have automatically going into your checking account usually get there 3-7 days after the actual date of payment, so before you begin the reconciliation process, make sure your withdrawals are up to date and open the For Review list in QuickBooks banking section for your checking account.

Click on match opposite every withdrawal from Square to match the information we synced with the actual withdrawals from Square into your checking.

Step 2_After Reconciliation

*Pro-tip: 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 your checking account to match the transactions on your monthly bank statement with the transactions we synced into QuickBooks Online. 

To reconcile an account in QuickBooks Online, click the Gear button. Then click on “Reconcile” under the “Tools”.


Use the “Account” drop-down as pictured on the screenshot to select an account. Have your bank statement handy to specify the “Ending balance” and “Ending date”.

 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.
square reconciliation in QuickBooks Online
square-reconciliation in QuickBooks Online

Congratulations! You are all set. 

By syncing into a bank account using the flow recommended in this guide, all of your online Sales and Expenses will be matched with your current checking statement. 

Bank balance and QuickBooks balance will be even and you will be able to easily keep track of your online Sales and Expenses.

Alexandra Kozyritskaya

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