Official organic regulation in Europe is based on the third-party certification system to guarantee organic products. Many critics and dissatisfactions have motivated the emergence of other guarantee systems, based on an intense implication of producers and, in some cases, consumers and other local actors, involved in localised agri-food systems. They are called Participatory Guarantee Systems (PGS), and are not recognised as valid guarantee systems by the official organic regulation. In the present paper, we analyse the main differences between the PGS and the third party certification system, deepening on their differentiated social and political implications. We conclude that the procedures behind PGS generate numerous positive impacts in the territories related to local producers (and consumers) empowerment and localised agri-food systems drive, while their implications make them not considered as a substitute to third party certification system, unless certain conditions of social consolidated groups and agroecological and food sovereignty perspective of food system take place.