Peri-urban agriculture (PUA) has been proposed as an important urban element to deal with the challenges of increasing poverty, food insecurity, and environmental degradation as particularly found in rapidly expanding cities of the developing world. However, farming in the peri-urban is under strong pressure from urbanization. The economic and social roles of farming need to be better understood in order to integrate peri-urban agriculture into urban planning. This study used multivariate techniques and Geographically Weighted Regression to analyze statistical data at a village and sub-district, to explore the varying relationships between agricultural activities and urban economic activities, urban poverty and informality, as well as food security. This method was applied in the Jabodetabek Metropolitan Area (JMA) with Indonesia’s capital Jakarta at its core, and it resulted in some important findings. First, PUA was more associated with the increasing low and middle class residential areas and the growing small-middle scale urban economic activities rather than development of tourism and larger traditional market facilities. Second, whereas PUA in the North of JMA was under pressure by the increasing poverty, in the Southeast of JMA it has expanded concurrently with increasing poverty. Third, PUA is strengthened by increasing informal activities in the peri-urban zone that offer alternative jobs and additional income for the farmers. Fourth, PUA in the surroundings of Jakarta as well as in the East and Northeast of JMA has contributed to increasing food affordability as well as strengthening food security policy. Based on these results, recommendations to maintain the PUA have been formulated to support its role for the peri-urban economy, reduce poverty, manage informality, and increase food security.