In general, when manually creating an order in dashboard, you should expect to manually set up the taxes too. The WooCommerce manual order creation page shouldn’t be expected to behave like a customer checkout, since it is not designed for that purpose. If you don’t want taxes, then, don’t press buttons that add taxes. (And if you did, then you can press the buttons to remove them afterwards).
Under the hood, when creating a manual order, when you calculate the taxes down in the product section, WooCommerce doesn’t actually provide any other details to the back-end code other than the product line items. i.e. The VAT number and any/all other billing fields aren’t actually sent to the back-end, and no hooks are provided to do so, so it’s not actually currently technically possible for the back-end to do anything with these details (until WooCommerce change how the admin page works).
Having said that, in response to previous customer requests, there is one exception we have been able to achieve, based upon what is possible. If you: 1) fill the billing address fields from an existing user (i.e. use the facility there to pre-fill the address from a WordPress user’s account details), and 2) if those fields include a VAT number (i.e. already saved on their account), then when you save the order, the first time, using the button for saving the new order in the top right, then the customer’s VAT number will be used to remove any taxes if there were any. So if you do want to automate the process, that is the way to do it (and as explained above, the only way that WooCommerce’s manual order page makes possible to do it).
Posted in: WooCommerce European (EU/UK/Norway/Switzerland) VAT Compliance