Understanding waste flows within an urban area is important for identifying the main problems and improvement opportunities for efficient waste management. Assessment tools such as material flow analysis (MFA), an extensively applied method in waste management studies, provide a structured and objective evaluating process to characterize the waste management system best, to identify its shortcomings and to propose suitable strategies. This paper presents the application of MFA to municipal solid waste management (MSWM) in Maputo City, the capital of Mozambique. The results included the identification and quantification of the main input and output flows of the MSWM system in 2007 and 2014, from the generation, material recovery and collection, to final disposal and the unaccounted flow of municipal solid waste (MSW). We estimated that the waste generation increased from 397×10³ tonnes in 2007 to 437×10³ tonnes in 2014, whereas the total material recovery was insignificant in both years – 3×10³ and 7×10³ tonnes, respectively. As for collection and final disposal, the official collection of waste to the local dumpsite in the inner city increased about threefold, from 76×10³ to 253×10⁶ tonnes. For waste unaccounted for, the estimates indicated a reduction during the study period from 300×10³ to 158×10³ tonnes, due to the increase of collection services. The emphasized aspects include the need for practical waste reduction strategies, the opportunity to explore the potential for material recovery, careful consideration regarding the growing trend of illegal dumping and the urgency in phasing-out from the harmful practice of open dumping.