The introduction of Activated Sludge Models No. 1 (ASM1) in the early 1980s has led to a decade-long experience in applying these models and demonstrating their maturity for the wastewater treatment plants’ design and operation. However, these models have reached their limits concerning complexity and application accuracy. A case in point is that despite many extensions of the ASMs proposed to describe N2O production dynamics in the activated sludge plants, these models remain too complicated and yet to be validated. This perspective paper presents a new vision to advance process modeling by explicitly integrating the information about the microbial community as measured by molecular data in activated sludge models. In this new research area, we propose to harness the synergy between the rich molecular data from advanced gene sequencing technology with its integration through artificial intelligence with process engineering models. This is an interdisciplinary research area enabling the two separate disciplines, namely environmental biotechnology, to join forces and work together with the modeling and engineering community to perform new understanding and model-based engineering for sustainable WWTPs of the future.