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Crop-based biogas energy production, in combination with electricity generation under subsidy schemes, is no longer considered a favourable business model for biogas plants. Switching to low-cost or gate fee feedstocks and utilising biogas via alternative pathways could contribute to making existing plants fit for future operations and could open up new space for further expansion of the biogas sector. The aim of this study was to combine a holistic and interdisciplinary approach for both the biogas production side and the utilisation side to evaluate the impact of integrating the biogas sector with waste management systems and energy systems operating with a high share of renewable energy sources. The geospatial availability of residue materials from agriculture, industry and municipalities was assessed using QGIS software for the case of Northern Croatia with the goal of replacing maize silage in the operation of existing biogas plants. Furthermore, the analysis included positioning new biogas plants, which would produce renewable gas. The overall approach was evaluated through life cycle assessment using SimaPro software to quantify the environmental benefits and identify the bottlenecks of the implemented actions. The results showed that the given feedstocks could replace 212 GWh of biogas from maize silage in the relevant region and create an additional 191 GWh of biomethane in new plants. The LCA revealed that the proposed measures would contribute to the decarbonisation of natural gas by creating environmental benefits that are 36 times greater compared to a business-as-usual concept. The presented approach could be of interest to stakeholders in the biogas sector anywhere in the world to encourage further integration of biogas technologies into energy and environmental transitions.