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It's possible that the paycheck was posted in a different bank account. This is the reason why you can't see the transaction in the register that you're looking at.
Let's open the paycheck again and check what account was used. Here's how:
If this is a recent paycheck and was not sent to Direct Deposit, you can delete and recreate it using the correct bank. Just click the Void or Delete button at the bottom of the paycheck. Then, select Yes to confirm that you want to remove it.
Once done, make sure the correct bank is assigned in your payroll settings. Here's how:
After that, recreate the paychecks to record the transactions in the correct register. Here's how:
If the transactions were send to Direct Deposit or not from the last period, the first option would not be applicable. In that case, you can create a journal entry to transfer the amount from one bank to another.
Here's how:
Let me share all these articles with you for additional details about the options I've mentioned above"
Don't hesitate to let us know in your reply if you're able to correct the paycheck and put it in the correct register. The Community is always here if you need anything else.