I appreciate you sharing complete details about matching bank deposits with several receipts and expenses, amberkab.
In QuickBooks Online, you can create a bank deposit and enter all items. Then, add the fees from there. This way, it'll match with what's in the real bank account entry with no invoices.
I'll guide you about how to do it.
- Click + New, then Bank Deposit.
- From the Account ▼ drop-down, choose the account you want to put the money.
- Scroll down to the Add funds to this deposit section.
- Enter all items.
- Enter the fee as a line item.
- Choose who the fee was from (for example, the bank charging you).
- Select Bank Charges from the Account ▼ drop-down.

- Enter the amount fee as a negative number. For example, if the fee was US $.50, enter –.50.
- Review the deposit total with the bank fee.
- Click Save and close or Save and new.
If there's an invoice, record the payment and post it to the Undeposited Funds account. Then, follow the steps above on how to add fees and post it the actual bank account.
Once done, match the deposit to the payment you've received through the Banking page. This links them together so you don't get duplicates.
Don't forget to reconcile your bank accounts every month. It'll help you compare each transaction with the ones entered into QuickBooks. Check out our complete reconciliation guide.
Feel at ease if you need assistance with how to match multiple transactions. I'll be here around to guide you always. Stay safe and more power to your business!