Carbon footprint (CF) is nowadays one of the most widely used environmental indicators. Six main methodological issues to take into account when collecting corporate data to be used for PCF studies were postulated and discussed in the present paper: fugitive emissions, credits from waste recycling, use of “equivalent factors”, reference flow definition, accumulation and allocation of corporate values to minor products. A big project with 18 wineries, being wine one of the most important agri-food products assessed through CF methodologies, was used to study and to exemplify these 6 methodological issues. The methodology discussed in this paper for the wine case study is widely applicable to any other product or industrial activity.