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Reconciling Offline payments with Online banking download in QB

When recording payments in that you have paid by other means and already recorded the payment in QuickBooks you have the option to 'Do not sync' in the payment confirmation screen in

In addition, you can consider posting the payments first in, syncing them to QuickBooks and matching them to the transactions that you download from your bank.

Please refer to the Help menu in QuickBooks for additional instruction for matching online banking transactions to existing transactions in QuickBooks