Fusarium root rot of maize and beans is a common problem in Taita District, Kenya causing reduction in yields to the small scale farmers. The pathogen attacks maize and beans at all growth stages causing rot at the seedling stage, yellowing of the leaves, stunted growth, and death if severe. Potentially effective crop rotations to maintain the pathogen at low levels are not currently practical due to the small size of farms while fungicides are out of reach to the small scale farmer due to high prices. This study aimed at assessing alternatives to fungicides in controlling root infection by Fusarium sp. in maize and beans. Field trials were done in Taita District where agriculture contributes to 95% of household income with very little or no soil fertility ameliorating inputs in farms. The following were tested in the trials; three types of inorganic fertilizers, cow manure, and Trichoderma seed coating. Planting was done during the long and short rains. Soil and roots were collected from the rhizosphere during harvesting and assessed for inoculum density while the roots were evaluated for incidence of infection by Fusarium spp. The most common species in both soil and roots were F. oxysporum (Schlecht) Snyd.et Hans. and F. sporotrichoides Sherb. Addition of soil ammandments had a positive effect of reducing root infection and in some cases lowering inoculum density in the soil. Of the four integrated soil fertility interventions, Mavuno had the highest yield and was the most effective in suppressing root colonisation by Fusarium spp