Safe fecal sludge management (FSM) - the hygienic emptying, transport, and treatment for reuse or disposal of fecal sludge - is an essential part of safely managed sanitation, especially in towns and cities in low- and middle-income countries with limited sewer coverage. The need for safe and affordable FSM services has become more acute as cities grow and densify. Hygienic pit-emptying uses equipment that limits direct human exposure with fecal sludge and hygienic transport conveys fecal sludge offsite for treatment. We evaluated whether a program of on-site sanitation infrastructure upgrades and FSM capacity development in urban Maputo, Mozambique resulted in more hygienic pit-emptying and safe transportation of fecal sludge. We compared reported emptying practices among multi-household compounds receiving sanitation upgrades with control compounds, both from the Maputo Sanitation (MapSan) trial at 24-36 months after the intervention. Intervention compounds (comprising 1-40 households, median = 3) received a subsidized pour-flush latrine to septic tank system that replaced an existing shared latrine; control compounds continued using existing shared latrines. We surveyed compound residents and analyzed available municipal data on FSM in the city. Due to the recent construction of the intervention, emptying was more frequent in control compounds: 5.6% (15/270) of intervention compounds and 30% (74/247) of controls had emptied their on-site sanitation system in the previous year. Among those compounds which had emptied a sanitation facility in the previous year, intervention compounds were 3.8 (95% CI: 1.4, 10) times more likely to have to done so hygienically. Results suggest that the construction of subsidized pour-flush sanitation systems increased hygienic emptying of fecal sludge in this setting. Further gains in hygienic emptying in urban Maputo may be limited by affordability and physical accessibility.