Yes, you can create an invoice for a back-ordered item while invoicing a customer. The stock on hand number will go into negative in the meantime until you restock.
Unfortunately, there is no separate back-order column on the Invoice.
If you're using the Estimate form in QBO, you can create multiple partial invoice from a single estimate. They call this Progress Invoicing feature in QBO. But still when you create an Invoice, there is no to back-order on the Invoice to your customer as you want. Just can't do it in QBO.
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