The relationship between temperature, high pH, desiccation, decomposition, pathogen destruction, and user operation in active double vault urine diverting (DVUD) composting latrines located in the Bocas del Toro region of Panama was assessed. Latrine samples were analyzed for temperature, pH, % moisture, carbon-to-nitrogen (C/N) ratio, and presence of specific pathogens. Surveys and visual inspections were used to verify use and type of dry material desiccant added. Measurements supported findings that compost latrines do not reach temperatures sufficient to destroy all pathogens. pH measurements showed that many latrines were operating within the range for ideal aerobic decomposition, a pH of 7.5-8.5, but only 17% of latrines measured pH 9 or above. Almost 100% of composting latrine users added sawdust and wood ash, to lower moisture level and provide carbon for decomposition. However, the recommended amount of desiccant added was insufficient to reduce moisture to the suggested 25% for pathogen destruction and C/N ratios remained in the range of raw human faeces. Importantly, pathogens, mainly helminths, were still present in compost stored for the 6-month contact time. The latrines have conflicting goals of pathogen destruction and aerobic decomposition. Recommendations are made regarding operation of composting latrines and disposal of composted material.