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Achieving safely managed sanitation (SMS) in rural areas has spurred innovation in toilet designs that provide on-site treatment of fecal sludge (FS), including the development of International Development Enterprise (iDE)’s alternating dual-pit latrine upgrade (ADP). ADPs treat FS by inactivating pathogens using storage treatment with lime; however, ADPs’ reduction in pathogenicity (and thus their associated public health benefit) has not yet been described in real-world pits at scale. We thus enumerate the fecal indicator bacteria Escherichia coli (E. coli) and fecal coliforms in 147 pits after two years of storage treatment with lime and compare detected concentrations to relevant standards. E. coli and fecal coliform concentrations indicated a risk to human health in 31% and 42% of sampled pits, respectively. Regression models described relationships between fecal indicator bacteria concentrations and measured factors (e.g., sludge pH, temperature) but did not reveal any meaningful associations. High rates of pit ineligibility also indicate that many ADPs are not operated as recommended. Results indicate a one-in-three chance that a household emptying their own pit would be exposed to health hazards and call into question the effectiveness of the standard two-year storage treatment in real-world applications. To improve rural SMS, various evidence-based recommendations are made. HIGHLIGHTS Fecal sludge stored in real-world alternating dual-pit latrines after treatment were enumerated for fecal indicator bacteria.; E. coli and fecal coliform concentrations indicated a risk to human health in 31% and 42% of sampled pits, respectively.; Households emptying pits after treatment have a one-in-three chance of being exposed to health hazards.; Many ADPs were not operated as recommended, reducing pathogen inactivation.;