The use of mathematical models is a well-established procedure in the field of (waste) water engineering to “virtually” evaluate the feasibility of novel process modifications. In this way, only options with the highest chance of success are further developed to be implemented at full-scale, while less interesting proposals can be disregarded at an early stage. Nevertheless, there is still lack of studies, where different plant-wide model predictions (effluent quality, process economics, and technical aspects) are comprehensibly verified in the field with full-scale data. In this work, a set of analysis/evaluation tools are used to assess alternative retrofitting options in the largest industrial wastewater treatment plant in Northern Europe. A mechanistic mathematical model is simulated to reproduce process behavior (deviation < 11%). Multiple criteria are defined and verified with plant data (deviation < 5%). The feasibility of three types of scenarios is tested: (1) stream refluxing, (2) change of operational conditions and (3) the implementation of new technologies. Experimental measurements and computer simulations show that the current plant´s main revenues are obtained from the electricity produced by the biogas engine (54%) and sales of the inactivated bio-solids for off-site biogas production (33%). The main expenditures are the discharge fee (39%), and transportation and handling of bio-solids (30%). Selective treatment of bio-solid streams strongly modifies the fate of COD and N compounds within the plant. In addition, it increases revenues (+3%), reduces cost (-9%) and liberates capacity in both activated sludge (+25%) and inactivation reactors (+50%). Better management of the buffer tank promotes heterotrophic denitrification instead of dissimilatory nitrate conversion to ammonia. In this way, 11% of the incoming nitrogen is removed within the anaerobic water line and does not overload the activated sludge reactors. Only a marginal increase in process performance is achieved when the anaerobic granular sludge reactor operates at full capacity. The latter reveals that influent biodegradability is the main limiting factor rather than volume. Usage of either NaOH or heat (instead of CaO) as inactivation agents allows anaerobic treatment of the reject water, which substantially benefits revenues derived from higher electricity recovery (+44%). However, there is a high toll paid on chemicals (+73%) or heat recovery (-19%) depending on the inactivation technology. In addition, partial nitration/Anammox and a better poly-aluminum chloride (PAC) dosage strategy is necessary to achieve acceptable (< 2%) N and P levels in the effluent. The scenarios are evaluated from a sustainability angle by using life cycle impact assessment (LCIA) in form of damage stressors grouped into three categories: human health, ecosystems quality, and resource scarcity. The presented decision support tool has been used by the biotech company involved in the study to support decision-making on how to handle future expansions.