Unapplied Invoice Payments

In most cases, ePayments received are automatically applied to an Invoice and the Invoice is closed. In some instances, payment exceptions - payments that don’t automatically apply to a Receivables invoice, will show up in the Bill.com Inbox and the payment will need to be manually processed.

Exception instances


Either the Paying company edits the amount of the eBill to more than the original amount, or the Receiving company edits the amount of the Invoice to less than the original amount. When the eBill is paid, the payment is more than the original or edited amount.

Double Payment

The Invoice is marked as Paid, but the Vendor pays the eBill, resulting in a double payment on the Receivables side.

ePayment Without an eBill

The Receivables company sends a PDF or paper bill, the Payables company processes it like a regular bill. The bill was never sent as an invoice/ebill. Since the two companies are linked, when the Payables company pays the bill, the payment will be sent as an ePayment.

ePayment with Vendor Credits Applied

Receivables company sends an Invoice to the Payables company. Payables company applies a Vendor Credit before paying the bill.

Connected vendor sends credit memo to their customer

The vendor sends a credit memo from their account which the Payables account can turn into a vendor credit for the vendor.

Applying payment

There are multiple options when processing payments from the Inbox.

Create an Invoice

Enter the credit amount from the payment which will show as available when creating the invoice.

Accept the payment without applying it to an invoice.

  1. Select Apply Invoice Payment
  2. Select Submit
  3. Select Done
  4. Delete if desired, or save for a later invoice

Delete the payment if you have already recorded a manual payment to the invoice or it is a double payment.

  1. Select Apply Invoice Payment
  2. Select Delete


  • Deleting an unapplied payment from the inbox doesn't reverse the payment. The payment will still deposit.
  • Once you delete an unapplied invoice payment from the Inbox, it can't be recovered. You'll need to record a manual payment to mark the corresponding invoice as paid.

If you don't see the described feature available in Bill.com, you may not have access to the feature based on permissions for your role and/or your plan doesn't have this feature. If you wish to get access to the feature, please review the available plans for Bill.com and upgrade accordingly or contact the Administrator of your Bill.com account. Changes in monthly user fees may apply.