How can I show an invoice as paid when it was accidentally paid from the wrong bank account?

Hi, @KIosue.

I can suggest a way to correct an invoice payment that was mistakenly paid from the wrong bank account in QuickBooks Desktop (QBDT) Mac.

Just a disclaimer, I'm only sharing the possible technical input on how we can achieve this. I recommend guidance from your fellow accountants while performing the steps below to ensure having accurate financial records. 

First, we need to set up a clearing account as a bank account in the Chart of Accounts.

1.  Navigate to Lists, then Chart of Accounts.
2. Click + at the bottom of the Chart of Accounts and enter information for the account.

Next, we can edit the written check to post to the clearing account. Then, we can write another check from the clearing account posting to Account's Receivable to select the correct vendor. 

When done, you can run reports to verify if the amounts reflect on the correct accounts. Let me add this article about customizing reports in QBDT Mac: Customize reports in QuickBooks Desktop for Mac.

We're always here in the Community should you need further assistance correcting invoice payments in QBDT Mac. We'll do our best to assist.

@KIosue 

There are a number of ways this can be accomplished.  Let's call the company that incurred the expense, Co. A, and the company that made the payment, Co. B. 

1)  In Co. B, there's no need to enter a bill.  The payment that was issued to the vendor should be assigned to an asset account.  You can do that by setting up Co. A as a customer and assigning A/R to the payment or create an other current asset account called 'Due from Co. A' and use that. 

2)  In Co. A, create a bank 'Clearing Account'.  Enter the vendor's bill and pay it using the bank Clearing Account.  Then, issue payment to Co. B and assign the bank Clearing Account as the expense account.  That will correctly record a bill under the vendor's account but issue payment to Co. B.  It will also zero out the Clearing Account.

3)  Assign the deposit in Co. B to the 'Due From Co. A' other current asset account or A/R, whichever asset account you used in step 1.  If you used A/R, don't forget to apply the payment to the "invoice" created by the payment.