The energy potential of high-organic loaded agro-industrial effluents receiving biological treatment is often neglected, particularly in emergent regions, because of different technical and regulatory drawbacks. In addition, small alternative bioenergy sources are forced to compete disadvantageously with conventional energy supply, hindering their more extended exploitation. Thus, smart strategies to prove the environmental/economic potential of biogas and sludge produced in biological wastewater treatment systems (Bio-WWTs) are required to promote them as truly sustainable energy sources. In this view, the present study depicts a refined methodological framework for a more appropriate appraisal of Bio-WWTs promoting bioenergy recovery. Life cycle assessment (LCA) and emergy analysis (EmA) methods were merged around the statement of some identified and stated Principle–Criteria of Sustainability (PCS) for this kind of “water-energy nexus.” As a result, a novel set of four single sustainability development indicators (SDIs) and one aggregated SDI were obtained to address sustainable conditions for valorization of bio-energy from agro-industrial Bio-WWTs. These indicators were made up of an environmental term coming from an LCA based on a system expansion approach as well as a second or “eco-economic” term obtained by means of EmA. This work introduces and shapes the “additionality” notion as an expression of overall sustainability and uses novel sustainability charts to interpret the obtained SDIs and their shifting or changes for different Bio-WWTs’ life cycle scenarios. The “proof of concept” of this methodology is discussed along the obtained results for two case studies in Colombia.