Abstract Bioenergy systems are expected to expand over the coming decades due to their potential to address energy security and environmental pollution challenges. Nevertheless, any renewable energy project can only survive if approved environmentally superior to its conventional counterparts. Life cycle assessment (LCA) is an internationally standardized and validated methodology to evaluate and quantify the environmental impacts of bioenergy systems. However, due to its methodological scope, the LCA method measures only the environmental consequences of the target products of energy systems. The LCA approach can neither allocate the environmental impacts at the component level nor measure the environmental impacts of intermediate products. These challenges can be substantially resolved by systematically integrating the LCA approach with the thermodynamically-rooted exergy, offering a powerful environmental sustainability assessment tool known as “exergoenvironmental analysis“. Due to the unique methodological and conceptual characteristics of exergoenvironmental analysis in revealing the possibilities and trends for improvement, it has recently received increasing attention to mitigate the environmental impacts of bioenergy systems. Therefore, this review is aimed to thoroughly summarize and critically discuss the evaluation of sustainability aspects of bioenergy systems based on exergoenvironmental analysis. The pros and cons of using exergoenvironmental analysis in bioenergy research are also outlined to identify possible future directions for the field. Overall, exergoenvironmental analysis can offer more detailed information on the environmental consequences of each flow and component of bioenergy production plants, thereby diagnosing the breakthrough points for additional environmental improvements.