Hello there, @Jennivdm.
You can create an invoice in Company A, then record it as bill in Company B. I can guide you on how to do it.
First, let's make sure to add Company B as a customer in Company A. Here's how:
- Go to the Sales menu.
- Choose the Customer tab.
- Select the New Customer button.
- Enter the details of Company B in the Customer Information window.

- Click the Save button.
Now, you can create an invoice.

On the other hand, you can enter Company A as vendor in Company B. You can follow these steps:
- Choose the Expenses menu.
- Select the Vendors tab.
- Click the New Vendor button.
- Enter the details of Company A in the Vendor Information window.

- Click the Save button.
Now, you can create a bill to record the invoice you'd receive from Company A.

You can create a journal entry to record the invoice payments in Company A and bill payments in Company B. Lastly, I'd recommend consulting with an accountant so you'd be guided accurately in tracking your VAT-related transactions.
Get back to us here if you have other questions or concerns. I'm always here to help.