QB Issue Resolution:

We can create a journal entry to offset the invoice and the bill that you’ve created. Let me show you how.

  1. Click on the plus (+) icon
  2. Select Journal Entry
  3. Select Accounts Receivable in line 1 and credit the amount of the invoice
  4. Select Accounts Payable in line 2 and debit the amount of the bill
  5. Click on Save and close.

You can receive the payment for the invoice and make payment for the bill using the journal entry.

I’d also recommend that you consult an accountant. He/she can give you professional advice on how to record a transaction like this.

Resolution for Issue 'Our customer paid directly to our supplier. What should I do exactly to record it correctly in our current version of QuickBooks Online Plus?' available: Yes (Solved).
Source: Intuit Community forum.

Our customer paid directly to our supplier. What should I do exactly to record it correctly in our current version of QuickBooks Online Plus?: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

Support for Invoice
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Error Recovery for Invoice [Canada]
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