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Buy nowHello droybal,
I too have been struggling with the same limitation you are, and that is it seems QuickBooks Desktop does not support custom fields at the invoice level. The best I can tell is that the custom field you created applies to the customer, not the invoice, and even though you can choose to display that field on the invoice, you are actually seeing data about the *customer*. This is why when you create a new invoice, this field auto-populates with the information from the underlying customer. When you change that value on the new invoice, this value will be saved back to the customer, and will become the new default value for that field for future new invoices, until changed again.
There may be some workarounds by first creating an Estimate or a Job, with the correct custom data attached (I know QB Desktop does support custom Job Types) and then generate your invoice from that. I haven't investigated all of the possibilities with this approach though.
Update: After working with this a bit more, I discovered (in Quickbooks Desktop 2020 at least) that when you fill in a custom field on a form (invoice, for example) and then save that form, you will be prompted on whether or not you want to permanently apply that value to the underlying customer. For my purposes, I always choose not to do this. Even if you do accidentally save the new value as the default for that customer, you can edit the customer, go to "Custom Fields" and remove the value saved in the field.