To most effectively integrate research across scales and disciplines, long-term system experiments (LTSE) can serve as a valuable tool in agroecological studies. In this paper, we discuss the role of LTSE in understanding agroecosystem function, as well as components to effective design these studies to further the implementation of agroecological practices. Further, we describe the contributions of long-term agricultural research sites (LTARs) to LTSE, as places at the crossroad of stakeholders and civil society, agricultural, economic, and social stakes, research and practical questions, and disciplines and methods (if not paradigms). In use ways, LTSEs and LTARs help overcome what we term the border problem of conventional agriculture research. Maintaining LTARs in a world dominated by short-term funding remains a key challenge to support agroecological research in need of multidimensional data, but is essential to address the need for interdisciplinary and transdisciplinary approaches to solve the wicked problems facing today's society.