In the transition towards climate neutrality, biorefinery models are considered promising alternatives to processes based on fossil fuels and non-renewable materials. This consideration is attributed to the reduction of dependence on non-renewable systems, in line with greener and lower impact technological strategies. However, they imply a profound transformation of the production system, as the variable and stochastic nature of certain renewable sources makes it necessary to have various tools to provide flexibility and optimize the system. Their market penetration is currently limited by their level of development and the regulatory and financial support to implement the paradigm shift. Traditional linear production is still more economically viable compared to circular production models, based on efficiency parameters achieved by years of manufacturing experience. To reverse this trend, it is necessary to leverage its benefits through the use of appropriate assessment tools, as these are the ones that could drive the move towards biorefineries. This is the focus of this research report, which reviews various evaluation methodologies and indicators to effectively evaluate bio-based process schemes. Life Cycle Assessment (LCA), Product Environmental Footprint (PEF), Green Chemistry Principles (GCP), certification scheme requirements and Circular Economy Action Plans are reviewed and integrated into a precise assessment framework. To determine their effectiveness, three biorefinery models were evaluated: valorization of apple vinasses, grape must and chickpea peel. Through the combined analysis of bio-based scenarios, it has been possible to identify their benefits, bottlenecks and limitations, and to validate a comprehensive assessment framework that allows an accurate, effective and conscious analysis of bio-based models, promoting their development and market penetration.