How do I pay the German tax office, and how do I avoid paying twice?

Two ways, never both at once, and card is not one of them. With a direct-debit mandate (SEPA-Lastschriftmandat) the tax office collects the amount on your return on its own schedule, usually around the due date. The mandate counts only once the office has confirmed it, which takes a few weeks after we lodge it, and the office requires the form signed by hand. Until it is confirmed, you transfer each return yourself to the tax office's account with the reference we show you (tax number, period, company). Once your dashboard shows that we collect by direct debit, do not transfer manually: the office then debits the same amount again, and getting the second payment back needs a written request, takes weeks, and small surcharges are sometimes held back. If your company banks outside the SEPA area, expect to stay on the transfer route. If you are unsure which state you are in, ask us before you transfer.