Resource efficiency in the agri-food sector is a global urgent issue considering the urbanisation phenomena, the increased nutritional needs, and the emergence of diversified dietary norms. Despite the ongoing progress in digital technologies that could enable resource-efficient operations in the sector, their effectiveness—even in developed countries—remains debateable mainly due to the limited understanding that further impedes their adoption by farmers. Among others, ease of access, training, and engagement with digital technologies appears to be challenging for most stakeholders, especially during the production (farming) stage. Specifically, in developing countries, that often encounter major natural resources challenges, the diverse socio-cultural background of the farmers hinders the adoption of digital technologies to perform highly automated and efficient agricultural operations for ensuring sustainability output. In this regard, we explore publicly available data sources (i.e., institutional reports, databases) to identify key challenges in adopting digital technologies for efficient resource use from a systems-level perspective. Thereafter, we map the determinant factors using the System Dynamics methodology in order to identify areas of interventions to limit natural resources’ appropriation and support agri-food sustainability.