Despite the global relevance, the microbial ecology of nonsewered wastewater during storage in containments remains poorly characterized. Anaerobic degradation is commonly assumed to occur during storage, yet the links between the microbial community and resulting greenhouse gas (GHG) emissions remain unresolved, especially for methanogenic pathways and the release of methane (CH4), an important GHG emitted during storage. This study combined amplicon sequencing and shotgun metagenomics of field samples from septic tanks in Southern Coastal British Columbia, Canada (n=18) and holding tanks in Kampala, Uganda (n=19) to characterize both the taxonomic composition and functional gene potential of the microbiomes in stored wastewater. Results showed similarly abundant community members at the phylum level (Firmicutes, Bacteroidota, Synergistota) alongside genus-level variability between locations and among individual containments in both study sites. Representation of energy metabolism pathways was consistent between individual containments in both study sites even where compositional taxonomic profiles differed. Further, methanogenic gene potential was consistently detected across depths in individual containments and across containments in both study sites. However, predicted methanogenic gene presence and physicochemical characteristics of stored wastewater, together with management practices, demographics and containment type did not fully explain measured CH4 emission variability. These findings illustrate the complexity of the physicochemical and microbiological processes involved in these degradation processes with important implications for interpreting field measurements and improving emission estimates from stored wastewater in septic and holding tanks. They suggest that emission predictions should focus on controls on substrate availability and regulation of microbial activity rather than community structure or functional potential alone.