QuickBooks Team
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Re: Customer unable to pay balance after partial payment made online

Thanks for joining this thread, Kitty111.

I appreciate you following the resolution steps provided by my colleague. Adding a manual payment directly to the Payments account can help resolve the issue.

The option to record a partial payment to the emailed invoices is unavailable at this time. Once a customer receives payment whether it’s partial or full, the transaction’s posting status will automatically be closed.

To track the remaining amount, manually add it in your QuickBooks Payments account.  Here's how:


  1. Log in to your QuickBooks company file.
  2. Choose the Banking tab located at the top menu bar.
  3. Scroll to the middle and select Make Merchant Service Deposits.
  4. Choose the Add Online Payments option, then input the deposit.

After entering it, this gives you an option to create an invoice. You’ll have to select the Need Invoice? link to make one.


Just in case, I also added a link with detailed information about recording Merchant Service deposits.


To record the amount, process it in your company file. Check out the steps provided by @JanyRoseB for visual reference or refer to this article for detailed instructions: Record a payment for an invoice. 


This information should get you on the right track. If you have further questions about the process, let me know by posting a comment below. I’m always here to help.