Land degradation, characterized by declining soil fertility and erosion, is a major constraint of maize productivity in Malawi, where more than half of the arable land is degraded. Although knowledge of soil fertility is critical for efficient input allocation, most smallholder farmers rely on subjective assessments of soil quality, which could potentially lead to imprecise decisions. This study examines how farmers’ perceptions of soil fertility and erosion influence input allocation and maize productivity among smallholder farmers in Malawi. Using plot-level data comprising 6370 maize plots from the Malawi Integrated Household Survey, we apply a Conditional Mixed Process estimator and stochastic frontier analysis to assess input use behaviour and technical efficiency. Results indicate that farmers allocate more labour and inorganic fertilizer to plots perceived as fertile, and adoption of improved maize varieties is lower on plots perceived as poor. Organic manure is more frequently applied on degraded plots to recondition the soils. Mean technical efficiency is estimated at 0.63, indicating substantial inefficiency relative to the production frontier. Further, technical efficiency declines with worsening soil conditions. These findings highlight sustainability risks associated with soil degradation and inefficient input allocation. Improved soil diagnostic services, integrated soil fertility management practices, and targeted extension programmes could promote sustainable land management and efficient matching of inputs to soil conditions.