QB Issue Resolution:

There are different ways to record donations, but usually a sales receipt is recommended.

The fee is considered a different transaction. If the customer donates $100, but you only get $97, they still donated $100, but your merchant banking costs are $3.

How you handle that depends on how the system you chose works.  Usually when working with a CC merchant service the fees are either taken out of the daily deposits or monthly.  If daily deposits, then include the payment in the deposit and add a negative line item for the fees.  If monthly then record the charge in your bank register like any other payment.

Resolution for Issue 'Are we suppose to input online charitable donations on sales receipt and how about the merchant fees taken out in each transaction – how do we do that in quickbooks?' available: Yes (Solved).
Source: Intuit Community forum.

Are we suppose to input online charitable donations on sales receipt and how about the merchant fees taken out in each transaction – how do we do that in quickbooks?: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

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