You reconcile accounts that have online banking the same way that you reconcile other banking accounts in QuickBooks, using the paper bank statement sent to you by your financial institution.
However, with online banking, QuickBooks helps you match the transactions from the electronic statements you download to the ones already in QuickBooks. By the time you reconcile, most of your transactions will have been checked against these electronic statements, so your records should be accurate and the process fast.
Usually, the information you download in electronic statements closely matches the transactions you enter into QuickBooks. Sometimes, though, your financial institution may process a transaction differently from the way you entered it into QuickBooks.
For example, suppose that you receive payments from five customers. In QuickBooks, you create one deposit for all five checks. However, when you actually take the checks to your financial institution to deposit, they process each one separately.
In this case, there is one entry in QuickBooks (for the total amount) but five entries in the electronic statement from your financial institution (one for each separate check).
In the Match Transactions window, you see:
Five unmatched transactions in the electronic statement, one for each check, since these amounts likely won't match any other entries in QuickBooks.
One unmatched transaction for the total amount in the register, since it likely won't match any other transaction in the electronic statement.
If this happens, it's best to change the QuickBooks transaction so that it agrees with your financial institution.
Working with online transactions in the Reconcile window
Troubleshooting reconciliation problems