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This article details how to record the following items in QuickBooks 2013 or later:
1. Go to the Banking menu > Make Deposits.
2. Select the payment(s) you want to record.
3. Click OK.
4. The deposit appears as a line item automatically, but you need to create a line item for the fee, if applicable. NOTE: You can confirm check fee amounts in the Merchant Service Center.
5. Click Save &Close.