Re-using faecal sludge (FS) to generate value has the potential to contribute towards solving the issue of long term sanitation solutions in growing urban areas across sub-Saharan Africa; however, hitherto, no design tools have been available that are capable of simulating a system involving economic factors, complex social issues and environmental circumstances. We hypothesized that Agent-Based Modelling (ABM), when deployed with appropriate rigour, can provide such a tool. Extensive field work was carried out in a Malawian city, investigating the adoption of Skyloo above-ground composting toilets by households, and the operation of the municipal FS site. 65 semi-structured interviews and 148 household interviews, together with observations, were carried out to characterize these processes, with the data acquired being used to construct two separate ABMs. The Skyloo ABM was run for various scenarios of start-up capital for business and payback of loans against the toilet cost to households. The municipal FS Site ABM was run for different patterns of dumping fee and enforcement structure. The field work demonstrated that there is potential for further expansion of FS reuse, with a market for agricultural application. The Skyloo ABM identified the significance of start-up capital for a business installing the toilet technology; the municipal FS Site ABM showed that existing fees, fines and regulatory structure were insufficient to reduce illegal dumping of FS to any useful degree, but that a monthly permit system would provide enhanced revenue to the city council compared with per-visit charging of disposal companies at the municipal FS site. Whilst each ABM ideally requires some additional data before full application, we have, for the first time, shown that ABM provides a basis for the simulation-based design of FS management systems, including complex social, economic and environmental factors.