Go to the Finanças Access page and enter your NIF and password;
Click on "Todos os Serviços" (All Services);
Click on "Recibos Verdes" (Green Receipts) and click "Emitir" (Issue);
Click on "Fatura-Recibo" (the common invoice known as a "Recibo Verde")
Choose the activity you provided.
Insert the NIF of the client and address, in case if the client is not in Portugal select the country first.
Briefly describe the service in the "Descição" box;
Insert the value in "Valor Base";
Select the VAT regiment (Exempt or Normal, depending on your case) under "Regime de IVA";
Apply by clicking the blue "Emitir" button and print the document, sign it and send it to your client.
NOTE If your annual income exceeds more than €200,000 you are obligated to hire an accountant.