Indonesia’s severely flawed centralized wastewater treatment system has caused economic and socioeconomic losses for decades. An alternative system has been called for under a national-scale program called Sanimas or Community-Led Total Sanitation (CLTS), which would cater to 50–100 urban families in every intervention with urgent needs through the operation of a decentralized wastewater treatment system. Through household participation, this program features a co-production system wherein the national-level government initiates and provides initial funding until construction, after which a community-appointed social organization takes over. This study implemented a multicriteria approach to assess sustainability in Sanimas communities in Jakarta: 67 in Menteng (Central Jakarta) and At-Taubah in Koja (North Jakarta). Connected households and facility-operating committees were questioned separately for their opinions on six aspects that explained the survival of the establishment of a facility: technical, management, community participation, financial, institutional, and environmental. We found that although the facility’s excellence and overall satisfaction with the program were unanimous, Koja and Menteng showed substantial differences in management, institutional, and financial aspects, largely due to administrative policies, payment contributions, and committee commitments. Interviews revealed that periodic testing of the treated water was neglected, against the provided guidance. In conclusion, communities have come to focus more on the technical functionalities of the installation, regardless of the state of the management, which is indisputable not only in Menteng but also in Koja. Finally, we argue that although decentralized systems can substitute centralized systems, they still require stringent and adequate support in quality control and troubleshooting.