In sub-Saharan Africa (SSA), farmers intercrop common beans with maize but apply inorganic or organic fertilisers targeting only maize. Effects of this practice on bush bean yield have not been fully evaluated with respect to input use and compatibility when intercropped with maize. An on-farm trial managed by smallholder community members was conducted to assess the influence of various soil fertility management options and cropping systems on the yield of two bush bean genotypes (SER45 and SER83) in two agro-ecological zones of Malawi. The farmer-managed trials were laid out in split-plot design, with the bean genotypes as main plots and a combination of the soil fertility management options (i.e., no input, manure, fertiliser and fertiliser + manure) and cropping systems (i.e., sole crop and intercrop) as subplots. The trials were affected by terminal drought and dry spells, but results show that manure and fertiliser application enhanced the resilience of the drought-tolerant bean genotypes.