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Yes, you can create a bill from a purchase order. When you enter a bill, the inventory count for the products will be affected. To ensure your records are correct, input the entry when you receive the items.
For your other concern, record the prepayment and then apply it to the bill. Then, associate the transaction to Accounts Payable. Allow me to help show the steps to do the process in QBO.
To link the bill to the prepayment:
However, if you want to bill the transaction to your customer, let me share the Enter billable expenses guide. It outlines the complete instructions to track expenses incurred and steps to apply them to invoices.
I'm also adding a link that can help manage prepaid items. It outlines the complete instructions on how to create a purchase up to linking the bill and check on the Bill Payments page: How to track your prepaid inventory.
Keep me posted if you have any clarifications or concerns. I’ll get back to answer them for you. Enjoy the rest of the day.