The difficulty to spatially link the process levels of organizing agricultural management with those of investigating biodiversity preservation creates a spatial scale mismatch which affects the effectiveness of agri-environmental policies. Starting from a literature review this study offers a panorama of the ways authors approach spatial scale mismatch and the solutions they propose to resolve it. We made the hypothesis that the authors rely, sometimes implicitly, on theoretical frameworks to propose their solutions. Only 15% of the references in which the authors examine the question of spatial scale mismatch show a systemic approach to the question, taking into account simultaneously ecological and managerial processes. We identify two major types of theory linked to the solutions proposed by the authors: those that refer to “multi-scale/multi-level” management for which hierarchy theory and landscape ecology are referred to explicitly; those that imply collective management and coordination, which refer to the theory of organization of biological systems and to social–ecological systems. These theories and their properties imply a change of paradigm which could allow for a better articulation between biodiversity and agricultural management. Based on this literature search we suggest that the problems in resolving spatial scale mismatch could be due to the fact that: (1) authors generally do not have a systemic approach since they consider ecological and managerial processes separately, and (2) terminology and theoretical frameworks are used inaccurately. While there are socio-economic difficulties in the implementation of biodiversity conservation programs in agricultural zones, there are also shortcomings linked to the theoretical representation framework. These shortcomings may hinder the articulation between ecological and managerial processes, this is why approaches are suggested here allowing for a better match between the representations of ecological and managerial processes