The European Environment Agency believes that circular economy strategies could substantially contribute to CO₂ emissions reduction. Therefore, it is necessary that the agro-industrial sector identifies sustainable technologies for side-stream management. The scope of this review was to compare the sustainability of available biological treatments for by-product biomasses and organic waste. A total of 147 studies, all Life Cycle Assessments (LCAs) and Techno-Economic Analyses (TEAs), were selected through PRISMA-ScR methodology, on Scopus and Web of Science, and were bibliographically mapped on VOSviewer (Version 1.6.20) Anaerobic digestion and integrated energy recovery systems were found to be the most environmentally robust options. Integrated biorefineries and multi-product systems have emerged as the highest long-term sustainability potential, especially when process integration and co-product recovery were also implemented. Importantly, the most sustainable systems were found to have required considerable start-up investments. Thus, sustainable deployment of biological treatment technologies was clearly dependent on time-consistent policy frameworks that have been fertile to capital-intensive infrastructures via incentives and fiscal measures and that have embraced circular bioeconomy systems. Finally, this paper has demonstrated that the sustainability of biological treatments has resulted from optimal relationships between biomass characteristics, system boundaries, process integration, and market value of co-product, while no single technology has been sufficient in isolation.