Does QB charge to have direct deposit through their website? I have not seen any charges, only the full amount I invoiced to the clients. Not sure if they charge later.

Hello there, @murphy-dvm-mph. Thank you for posting in QuickBooks Community!

Yes, QuickBooks Payments charges a fee each time you process a transaction. It depends on how you process the payment and its rate per transaction. When sharing an online with your customer, who then pays you using an ACH bank transfer or credit or debit card will be in 2.9% + 25¢.
 

You can take a look at the chart below:

You'll see the charges as long as you've already set up a QuickBooks Payments account and the payments have been processed.
 

You can learn more about payment processing fees by utilizing the resources below:

• What are the fees for QuickBooks Payments?
• Frequently asked questions

• Learn how to check when QuickBooks deposits customer payments into your bank account.

I'll be here if you have other concerns. Take care and have a good one!

@murphy-dvm-mph 

Do you have a QuickBooks Payment account or use another payment processor? How did your client pay your invoice? Did they send the payment with ACH directly to your bank account?