A container-based toilet (CBT) is a type of ecological toilet that allows users to compost their feces. During emptying, bucket washing, and composting operations, operators are exposed to microbial risks. This paper aims to evaluate these risks using the Quantitative Microbial Risk Assessment (QMRA) method. Nine pathogens prevalent in Haiti were targeted: Ascaris lumbricoides, Campylobacter spp., Cryptosporidium parvum, Escherichia coli O157:H7, Giardia intestinalis, poliovirus, Salmonella spp., Shigella spp., and Vibrio cholerae. Information regarding pathogens' concentration in feces came from scientific literature data. The exposure scenarios considered were those in which operators accidentally ingested a low dose of feces during the aforementioned operations. A Monte Carlo simulation was conducted to address uncertainties. The results showed that the probability of infection is highly elevated, while the probability of illness is generally moderate or minor, except for poliovirus and Ascaris. Preventive measures can be implemented to reduce these risks during various operations, such as wearing gloves, disposable protective masks, and appropriate clothing. It is up to the political authorities to develop guidelines in this regard and to organize awareness-raising activities with the help of local organizations mandated by the relevant authorities to ensure the safer use of technology by households.