With the trends of increasing flood risk due to climate change and rapid urbanisation in many parts of the world, property level mitigation efforts have become more relevant in flood risk management. However, the flood mitigation behaviour of business owners is an understudied aspect of risk reduction. This article employs the Protection Motivation Theory framework to identify critical factors that determine the flood damage mitigation behaviour of micro, small and medium enterprises in three neighbourhoods of Kampala, Uganda. We conducted a sample survey of micro to medium-sized business owners in two informal areas and one formal area in Kampala. Our analysis established that businesses of all sizes adopted structural measures and that micro-enterprises (0–4 employees) were more likely to implement non-structural measures than small businesses. Financial losses, risk aversion, and perceptions of flood likelihood all showed positive relationships with flood damage mitigation actions. Many businesses indicated that relocation is an inefficient and costly measure, though one that is easily self-implementable. Information-seeking behaviour and receiving flood-related information stimulated businesses to mitigate, though few businesses have regular access to helpful information regarding flood mitigation measures, especially concerning non-structural measures. These insights provide a basis for crafting business resilience-building policy and strategies considering increasing climate change-induced flash-flood risk in Kampala and other similar contexts.