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Background  Several studies that aim to enhance the understanding of malaria transmission and persistence in urban settings failed to address its underlining complexity. This study aims at doing that by applying qualitative and participatory-based system analysis and mapping to elicit the system’s emergent properties.    Methods  In two experts’ workshops, the system was sketched and refined. This system was represented through a causal loop diagram, where the identification of leverage points was done using network analysis.    Results  45 determinants interplaying through 56 linkages, and three subsystems: urbanization-related transmission, infection-prone behaviour and healthcare efficiency, and  Plasmodium  resistance were identified. Apart from the number of breeding sites and malaria-positive cases, other determinants such as drug prescription and the awareness of householders were identified by the network analysis as leverage points and emergent properties of the system of transmission and persistence of malaria.    Conclusion  Based on the findings, the ongoing efforts to control malaria, such as the use of insecticide-treated bed nets and larvicide applications should continue, and new ones focusing on the public awareness and malaria literacy of city dwellers should be included. The participatory approach strengthened the legitimacy of the recommendations and the co-learning of participants.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12936-021-03851-7.

Emerging properties of malaria transmission and persistence in urban Accra, Ghana: evidence from a participatory system approach