Nearly half (46%) the world’s population is now served by non-sewered sanitation. In urban areas of low- and middle-income countries, this translates to onsite storage of wastewater in tanks and pits until it can be collected and transported by road to treatment, which is commonly referred to as fecal sludge management. The microbial communities that develop during storage of this wastewater remain understudied, leaving practitioners and scientists to speculate on best management practices such as downstream treatment and climate mitigation measures. In this study, we collected samples from 135 randomly selected containments across the city of Lusaka, Zambia, and evaluated statistical relations of 16S rRNA gene sequence data to types and volume of wastewater going into containments, disturbances (i.e., emptying events), characteristics of accumulated wastewater during storage, and metrics of downstream treatment processes. At the phyla level, 80% of the identified microorganisms belonged to Firmicutes, Proteobacteria and Bacteroidota. Focusing in at the genera level, microbial diversity and composition were statistically related to volumes of water usage, properties of wastewater in containments (TOC, NH4, TKN, pH), and metrics of stabilization and dewatering performance. In Lusaka, a core community was identified with 104 of the 1,247 identified genera being present in >90% of the containments. In contrast, 936 genera were present in <60% of the containments, indicating that niche or transient organisms may also be important in unravelling metabolic processes such as sulfur reduction, methanogenesis, and ammonia tolerance. Community similarity was independent of time since last emptied, indicating stability of microbial communities over time. Identified metabolic differences between pit latrines (i.e., less water usage) and septic tanks (i.e., more water usage) indicate that methanogens more actively convert organic matter to methane in the more dilute wastewater, which could be globally relevant for greenhouse gas mitigation from non-sewered sanitation.