Southern Malawi is continuously affected by tropical cyclone-related floods (TCRFs), which have negative consequences on households' livelihoods, thereby displacing most households to neighbouring communities of Mozambique. The TCRFs have further threatened national, regional, community, and household food security agenda, which is already constrained by poverty, poor agricultural practices, low use of improved varieties, unaffordable inorganic fertilizers, and fragmenting landholding sizes. Accordingly, households have indigenously engineered resilience-based Sustainable Landscape Management (SLM) practices, like intercropping, agroforestry, cover cropping, and soil and water conservation practices, against the adverse effects of TCRFs on-farm productivity. Hence, this study examines the effect of TCRFs and SLM adoption on-farm productivity. While using rigorous endogenous switching regression econometric tools, the study finds TCRFs reducing farm productivity by 27 percent. After SLM adoption, the study observes farm productivity enhancement by 29–126 percent when households adopt at least one SLM practices under varying degrees of TCRFs. Despite the highlighted advantages of SLM adoption, female farmers are less likely to adopt SLM practices because they do not have access to productive resources. Hence, the study proposes the need of gender targeted extension services, accompanied by some seed capital for SLM adoption. Besides, there is need to sensitize farmers on the complementarities between inorganic fertilizer and SLM practices. Lastly, future studies should assess the effect of sustained SLM adoption or dis-adoption and input intensification on farm productivity.