Agricultural waste is a huge pool of untapped biomass resources that may even represent economic and environmental burdens. They can be converted into bioenergy and bio-based products by cascading conversion processes, within circular economy, and should be considered residual resources. Major challenges are discussed from a transdisciplinary perspective, focused on Europe situation. Environmental and economic consequences of agricultural residue management chains are difficult to assess due to their complexity, seasonality and regionality. Designing multi-criteria decision support tools, applicable at an early-stage of research, is discussed. Improvement of Anaerobic Digestion (AD), one of the most mature conversion technologies, is discussed from a technological point of view and waste feedstock geographical and seasonal variations. Using agricultural residual resources for producing high-value chemicals is a considerable challenge analysed here, taking into account innovative eco-efficient and cost-effective cascading conversion processes (bio-refinery concept). Moreover, the promotion of agricultural residues-based business is discussed through industrial ecology, to promote synergy, on a local basis, between different agricultural and industrial value chains. Finally, to facilitate a holistic approach and optimise materials and knowledge flows management, the connection of stakeholders is discussed to promote cross-sectorial collaboration and resource exchange at appropriate geographic scales.