The combination of techno-economic process modelling and life cycle assessment is an integrated methodology that addresses quantitative operational data, and evaluates the emissions associated with any process under development. In particular, the valorisation of waste streams within the context of the circular economy could be considered a valid and promising approach, especially regarding techno-economic and environmental indicators. This manuscript aims to evaluate the integral valorisation of apple pomace from the processing industry into bioethanol, and vinasses (a byproduct of the distillation process) into biogas and digestate as biofertiliser. In addition to biogas production, lagooning and composting were considered as strategies for vinasse management. After the conceptual design of the process options was completed, the environmental profile of bioethanol production was estimated across different scenarios. When biogas production was integrated to reduce the biorefinery’s energy demand, the carbon footprint was 1.13 kg CO2eq∙kg−1. This footprint increased to values around four when lagooning and composting were used as vinasse management strategies. Although the economic dimension posed a significant limitation due to high investment costs, the eco-efficiency analysis showed that the scenario of the co-production of bioethanol and biogas is the best alternative. Despite the promising results, further research is needed to explore the recovery of additional co-products to develop a high-potential strategy for apple pomace.