Bacterial wilt, caused by Ralstonia solanacearum, is a major tomato disease in tropical and subtropical regions. It is difficult to be managed, since no single measure confers significant contribution for disease control. Among the cultural practices available for disease management, bokashi provides nutrients to the plants, increasing the microbial biomass, improving the quality of the soil and, in some cases, protecting plants against diseases. In this work, we evaluated the effect of three different bokashis (Embrapa-BE; poultry-BP and cattle-BC) in two soils artificially and naturally infested with R. solanacearum, on the suppression of bacterial wilt in tomato. Disease control is discussed upon measurements on the contents of microbial biomass carbon (MBC), on total organic carbon (TOC), on basal respiration (BR), on metabolic coefficient (qCO2) and on microbial coefficient (qMIC). The experiment was implemented in greenhouse, with completely randomized design and factorial arrangement of treatments 2 × 3 (two soils × three bokashis). Disease suppression, assessed through wilt incidence 20 and 30 days after transplanting, was better observed in the naturally infested soil, where BP and BE were more efficient in controling the disease. TOC contents were higher in the artificially infested soil compared to that naturally infested, whereas the qMIC presented higher value for the naturally infested soil, which had greater contribution of MBC. Higher rates of BR and qCO2 were observed for the naturally infested soil with BC, probably indicating high plant stress caused by the disease in this treatment. Moreover, a high and positive correlation coefficient was found between the variables qCO 2 and the number of infected plants at 30 days after transplanting. In the artificially infested soil, a negative correlation was found between the number of infected plants at 20 days after transplanting and TOC.