Septic tanks are widely deployed for off-grid sewage management but are typified by poor treatment performance, discharge of polluting effluents and the requirement for frequent de-sludging. The Solar Septic Tank (SST) is a novel septic tank design that uses passive heat from the sun to raise in-tank temperatures and improves solids degradation, resulting in a cleaner effluent. Treatment has been shown to exceed conventional systems, however, the underlying biology driving treatment in the system is poorly understood. We used next generation sequencing (Illumina Miseq (San Diego, CA, USA), V4 region 16S DNA) to monitor the microbiology in the sludge and effluent of two mature systems, a conventional septic tank and an SST, during four months of routine operation in Bangkok, Thailand, and evaluated the ecology against a suite of operating and performance data collected during the same time period. Significant differences were observed between the microbiome of the sludge and effluent in each system and the dominant taxa in each appeared persistent over time. Furthermore, variation in the microbial community composition in the system effluents correlated with effluent water quality and treatment performance parameters, including the removal of chemical and biochemical oxygen demand and the concentration of fecal and total coliforms in the effluent. Thus, we propose that a wide-scale survey of the biology underlying decentralised biotechnologies for sewage treatment such as the SST could be conducted by sampling system effluent rather than sampling sludge. This is advantageous as accessing sludge during sampling is both hazardous and potentially disruptive to the anaerobic methanogenic consortia underlying treatment in the systems.