Carbon footprint (CF) is nowadays one of the most widely used environmental indicators. The scope of the CF assessment could be corporate (when all production processes of a company are evaluated, together with upstream and downstream processes following a life cycle approach) or product (when one of the products is evaluated throughout its life cycle). Our hypothesis was that usually product CF studies (PCF) collect corporate data, because it is easier for companies to obtain them than product data. 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. One of the main conclusions was that indeed, it is possible to collect corporate inventory data in a per year basis to perform a PCF, but having in mind the 6 methodological issues described here. In the literature, most of the papers are presenting their results as a PCF, while they collected company data and obtained, in fact, a “key performance indicator” (ie., CO2eq emissions per unit of product produced), which is then used as a product environmental impact figure. The methodology discussed in this paper for the wine case study is widely applicable to any other product or industrial activity.