This study focused on the development of an innovative sludge treatment unit that is based on the microwave irradiation technology. The technology provides a rapid and efficient option for sludge treatment in isolated conditions such as slum, emergency, and similar situations. The microwave based technology forms part of the eSOS (emergency sanitation operation system) concept that promotes an integrated sanitation approach in which all components of the entire sanitation chain are planned holistically. Besides, the study addresses the deficiencies associated with the poor choice of emergency sanitation technology options by proposing a methodology that is based on compensatory multi-criteria analysis. This study contributes in providing solutions towards improved sanitation in complex scenarios, especially the management of faecal sludge in emergency and slum conditions.