To a large share of people living in cities of the “Global South”, the lack of access to basic services and infrastructures have turned the urban habitat into a public health hazard. Notably, the lack of basic sanitation infrastructures is a key risk factor to several infectious diseases. For some decades now, slum upgrading projects have been implemented globally as a strategy to enhance living conditions in impoverished settlements, by bringing in basic infrastructures while preserving the human settlement. These interventions have had different levels of success, which certainly depends on the project’s ability to reach out slum dwellers and understand their needs. This study puts forward empirical evidence obtained from 1,721 household surveys in Nairobi (Kenya) and Abidjan (Côte d'Ivoire) to inform the design and planning of sanitation infrastructures in a way that accounts for safety issues, which seem recurrent in the context of informal settlements. In this sense, toilet location significantly affected the users’ perception of safety and, consequently, the risk of diarrheal diseases. Current slum upgrading frameworks must move away from a purely quantitative perspective of service provision. The sole availability of improved services represents a theoretical improvement; in practice, however, the health benefits of these same improved services may be null if the targeted populations do not feel safe to use them.