This study sought to understand the determinants of household’s choices for fecal sludge (FS) emptying to help fighting against unhygienic/unsafe practices and environmental pollution. A cross-sectional mixed study used in the municipality of Yopougon (Abidjan, Côte d’Ivoire), involved surveys (559 household), and 24 semi-structured interviews. Adjusted odds ratios (aORs) from logistic regressions indicated the variables significantly associated with these practices while thematic content analysis helped assessing stakeholders’ perceptions. Respondents (47.6%) reported unhygienic/unsafe emptying, mainly direct FS discharge into open drains or the immediate environment via illegal toilets/pits connections (38.1% out of 47.6%). Household heads with a high monthly income (aOR = 0.59; 95% CI 0.35–0.98; p = 0.04), house ownership (aOR = 0.27; 95% CI 0.15–0.47; p < 0.001) and distance to a water body (aOR = 0.03; 95% CI 0.009–0.12; p < 0.001) were the main explanatory variables, significantly reducing the likelihood of unsafe emptying. This likelihood increases when the household is close (≤ 100 m) to gully/gutter (aOR = 1.73; 95% CI 0.99–3.03; p = 0.05). Our recommendations for improving sanitation in low-income settings include reducing environmental pollution caused by unhygienic/unsafe emptying practices requires, enhancing and enforcing current regulations and making implementing texts effective, raising public awareness focusing on the benefits associated to hygienic sanitation practices, and subsidizing sanitation interventions for the poor that includes homeowners.