Discussions on food security in the Global North have raised questions about the capacity of peri-urban organic agriculture to provide sufficient healthy food for the urban market. Dealing with food security requires more attention to how to protect peri-urban organic farming systems from urban pressures while strengthening the sustainability of local food systems. Given that short food supply chains (SFSCs) have been proven to be effective at reconnecting people with food production, this study focuses on identifying the barriers that hinder their development and the opportunities derived from the comparative advantage provided by their urban proximity. This study is based on documentary and empirical research addressing food supply chain characteristics in the organic sector. This study is focused on Mediterranean peri-urban agriculture, where, historically, there have been close relationships between the city and the countryside. These relationships are based on the fact that many cities are traditionally located next to areas of high agricultural activity, where a wide variety of vegetables is produced almost continuously due to the relatively mild winter climate. This study deals with two medium-sized metropolitan areas in Andalucía in the south of the Iberian Peninsula—the coastal city of Málaga, which is of a tourist-residential nature, and the inland urban agglomeration of Granada. Our research shows, when compared with other studies, that the local organic food sector seems to have great potential to find innovative solutions based on a collective approach, local embeddedness, and collective knowledge and by prioritizing horizontal and sustainable processes at the local/regional scale.