QB Issue Resolution:

On the receive payment screen, enter the full amount of the invoice so the invoice can be paid. On the make a deposit screen, check off the customer payment being deposited, then on the next line enter the credit card discount as a negative number. This will match what Braintree is depositing.

Resolution for Issue 'How should I apply a payment to an invoice when the fees are deducted prior to the bank deposit (Braintree deposits are less than the invoice because the 2.9% fee) When receiving Braintree deposits, the fees are already removed from my customer payments. So when applying the payment the amount is less than the invoice. What is the best way to apply these Braintree payments to my invoices?' available: Yes (Solved).
Source: Intuit Community forum.

How should I apply a payment to an invoice when the fees are deducted prior to the bank deposit (Braintree deposits are less than the invoice because the 2.9% fee) When receiving Braintree deposits, the fees are already removed from my customer payments. So when applying the payment the amount is less than the invoice. What is the best way to apply these Braintree payments to my invoices?: 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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