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Bioenergy can significantly contribute to facilitating the transition to a self-sufficient low-carbon energy sector in Europe. The establishment of sustainable bioenergy systems needs ex-ante analysis that considers specific contexts and potential trade-offs, including competing uses of natural resources such as land, water and energy. The use of marginal and underutilized lands has been emphasized as a valuable strategy to overcome the food vs fuel paradigm and the direct and indirect land use change that can derive from the cultivation of bioenergy crops. Nevertheless, the fragmentation of these lands can significantly affect the energy efficiency of the systems, due to increased energy needs for inputs and transport, with trade-offs on the carbon footprint of the pathway. This study performs an ex-ante assessment of the sustainability of a short bioenergy pathway through the Land-Water-Energy nexus approach, by the iterative use of a web geographic information systems platform, developed on the methodology of the Global Bioenergy Partnership. The simulations show that the production of bioenergy from oilseed crops is expected to reduce greenhouse gas emissions by 73% compared to the reference emission value for fossil fuels in transport. The platform proofs to be effective and user-friendly for assessing and optimizing the intricate interlinkages among the various nexus domains that coexist within the bioenergy system based on the cultivation of underutilized land. Its use can facilitate the nexus operationalization serving as a timesaving decision-support tool for the development of sustainable bioenergy systems that contribute to the transition towards a low-carbon energy sector in Europe. [Display omitted] • Bioenergy production using undertuilized land can support a low-carbon transition of the energy sector. • A web-GIS platform was proposed to incorporate the Land-Water-Energy nexus of bioenergy. • The GBEP sustainability indicators was implemented for the assessment and monitoring. • Nexus assessment go beyond the compartmentalization of disciplinary silos. [ABSTRACT FROM AUTHOR]