Declining soil fertility is a major constraint limiting African agriculture. In a four-year (2007-2011) on-farm study in Malawi, we compared the effects of compost (bokash and liquid manure) and compost (bokash) in combination with low doses of inorganic fertilizer with recommended inorganic fertilizer rates on the performance of three maize genotypes. Compost use resulted in increases in soil organic carbon, total nitrogen, available phosphorus, and soil pH. Chemical analysis of both bokash and liquid manure indicated the need to improve compost quality. In low rainfall areas and sites characterized by poor soils but with good quality compost, maize yields did not show significant differences between chemical fertilizer and bokash plus urea. Although it was not possible to quantify soil-water balance studies in these on-farm trials, it can be assumed that bokash helped in soil-water conservation in low rainfall areas, thereby, improving the ability of maize to withstand conditions of water stress compared with the effects of NPK A. R. Ngwira et al. fertilizer. While SC627 gave 29% higher yields under chemical fertilizer compared with bokash and urea, yields of both local and ZM621 were similar between the two treatments, suggesting that local and ZM621 are less responsive to fertility inputs. Our study showed that for maize hybrid variety, SC627, lower vulnerability to low yields is obtained from the application of chemical fertilizer. For both local maize and OPV variety ZM621, less risk of a lower yield is obtained when the plots received applications of a combination of bokash and urea rather than a total reliance on chemical fertilizer. The results of this study call for a more nuanced approach than the current recommendation permits.