How to Charge Customer for Shipping When Invoice is Already Paid In Full

Since the invoice is already paid in full, editing the invoice to add the shipping fee is not advisable.
As an alternate solution, create an expense item: Other Charge for us to use in the Items tab of the Invoice.
A. Create an Other Charge Item
1. Navigate to Lists > Accounting > Items > New. 2. Click on Other Charge > For Sale link.
3. Enter an item name.
4. Hit Save.
B. Create an Invoice
1. Navigate to Transactions > Sales > Create Invoices.
2. Select the Customer.
3. Under Items tab, select the newly created Other Charge item. 4. Input the correct shipping amount.
5. Hit Save.