How do I record a transaction from Stripe (with fees) that is a batch deposit from invoices that were created and paid in Dubsado?

You're on the right track with depositing your payments, melterang. To match the total amount of the deposit, you'll have to add the Stripe fees as a negative amount in the Add funds to this deposit section. This ensures your customer's balance is correct and keeps your books accurate.

When you deposit payments in QBO from Undeposited Funds, you're correctly moving them out of the holding account. However, the deposit total won’t match your bank account because Stripe fees aren’t included; this is what’s causing the discrepancy. The totals shown in QBO are the gross payment, not the net amount after fees. To correct this, you'll have to include the fees as a negative amount in the Add funds to this deposit section. Here's how:

1. Go to + Create and select Bank deposit.
2. In the Select the payments included in this deposit section, place a check mark to select the payment you want to deposit.
3. From the Add other funds to this deposit section, enter the amount of the Stripe fee charged to you as a negative amount.
4. From the Account section, select the Expense account you usually use in tracking bank fees.
5. Verify that the deposit amount is correct.
6. Choose Save and close to record the transaction. 

If you have any further questions about handling your deposits, feel free to reply in the comments. We're here to help.