I have an employee who didn't get paid through direct deposit. I have verified his account information and routing number, and it all is correct. The employee also verified the numbers on their end and it is all correct. The employee contacted their bank, and they stated that there is no pending direct deposits on his account. Quickbooks says that it has been sent and cleared.
We were on the quickbooks online version last pay period, and switched to the desktop version this pay period. I had to reload all the employees informations, and everyone got paid this week via direct deposit, except this one employee.
First, I would ask the employee to provide a cancelled check so that you can double check the account and routing number. Secondly, I would ask for the employee for a copy of his bank transactions. Intuit obviously debited your account for the direct deposit and it went somewhere. The question is where. You can try voiding the check and sending the payroll information to Intuit. They may be able to cancel the direct deposit and/or reverse it if not a lot of time has lapsed.