How to Fix Reconciliation Differences in QuickBooks Online
Ever experienced that frustrating moment when you’re almost done reconciling an account, only to find there’s still a difference between your book balance and your bank statement?
(Screenshot of the reconciliation screen. Data scrubbed for confidentiality.)
You’re not alone. This is one of the most common issues small business owners face in QuickBooks Online (QBO).
Hidden Cause: A Transaction Marked as “Reconciled”
One hidden cause could be that a transaction was accidentally labeled as reconciled.
(Screenshot of a transaction from the Account History view. Steps on how to access this screen shown later.)
When this happens, QuickBooks automatically excludes it from the list of transactions during your next reconciliation. That means even though the transaction exists in your books, it won’t appear on your reconciliation screen.
(Screenshot of the reconciliation screen.)
Real-World Example
During a month-end reconciliation, a $2,800 deposit was missing from the list of transactions.
To fix it, the user manually added the transaction using the Bank Deposit feature.
Before:
(Screenshot of a segment of the reconciliation screen, before the transaction was added manually.)
After:
(After the transaction was added manually.)
The result? A duplicate entry of the same $2,800 deposit, making the reconciliation off by exactly that amount.
How to Spot the Error
The easiest way to find these issues is to review the Account History (also called the register) of the account you’re reconciling.
Here’s how:
Go to Transactions → Chart of Accounts
Use the search bar to find your account
Click Account History
From there, review the list of transactions and look for any that match the difference amount. In this example, one transaction was already marked with an “R” (reconciled), which is why it didn’t appear on the reconciliation screen
(Screenshot of the double entry from the Account History view. Notice that the original transaction is labeled “R”.)
How to Fix It
To correct the issue:
Delete the duplicate transaction that was manually added.
Remove the reconciled status from the original transaction so it appears correctly during your next reconciliation.
Pro Tip:
Before reviewing individual transactions, always confirm that your beginning balance in QBO matches your bank statement.
In this example, the beginning balance of $2,800 didn’t match; a red flag that could have saved time if checked first.
(Screenshot of the reconciliation screen.)
Note: If you remove the reconciled label from a transaction that was part of a previous reconciliation, re-run your reconciliation report to confirm everything still ties out.
Final Thoughts
Reconciliations are one of the best ways to keep your books clean, but they can be tricky when transactions are accidentally marked as reconciled or duplicated. But once you know where to look, fixing them is straightforward.
Book Your Free 30-Minute Consultation
If you’d like help reviewing your QuickBooks Online setup or understanding your reconciliation reports, book a free 30-minute consultation with me.
We’ll look at your books together, identify any hidden issues, and make sure you’re set up for smoother, stress-free bookkeeping going forward.