I have a customer that paid through ACH payments. The payment was deposited, but was later disputed and rejected due to insuffienct funds

Thank you for bringing this to our attention, Liberty. 

I’ll provide the information you need to resolve the rejected payment. 

Insufficient funds indicate that your account balance is not enough to cover the necessary fees. Because the customer payment was disputed, you'll have to cover the associated fee.

Since you encountered this, start by checking the balance of the bank account linked to your QuickBooks Payments account to see if the funds are available.  

If the funds are available or if you wish to pay an outstanding balance with a credit card, contact our live support team. Be sure to have your Merchant Account information and case number ready to expedite the resolution process.  

I'll add this article for more info: Fix rejected ACH payments. 

Now, since this is an ACH payment, you'll need to record it as a returned payment or a bounced check to ensure your records are accurately accounted for in QuickBooks.  

For further concerns about managing the rejected payments. I'll be here to ensure you have all the help you need.