How to record NSF check already applied to invoice in Quickbooks online?
1. enter a payment in the bank register in that amount and use a bad debt expense account in the account block (create one first if you need to in the chart of accounts), change the check number block to NSF 2. do the same thing as a payment if the bank hit you with bounced check fees
at this point your QB bank register will match the banks accounting
3. Now it is up to you, most counties have a legal procedure you must follow for bounced checks, then if the procedure does not work you can turn it over to the county attorney for processing - so you should get that procedure because if you do not follow it, when you do go to the county attorney they will want you to start all over.
as part of that procedure I create a new invoice, I create and use an item called NSF check-fee which has an income account selected on the item screen. list that item and enter the amount of the bad check use that same item again and enter your company bounced check fee and/or the banks fee amount
And don't forget the legal requirement to have a sign posted that states what your bounced check fee is. Always good to have a pic in your phone of that sign at the check out counter. First time I went to the county attorney to submit a bounced check they asked.