The domestication of Jatropha curcas L. in the Brazilian territory has been boosted by its great potential in the production of grains, oil and, in particular, its adaptation in different soil and climatic conditions. The aim of this research was evaluate the soil biological quality through the soil microbial biomass carbon and its indices derivate (metabolic and microbial quotient) under J. curcas intercropping with many forages species, legumes and annual crop rotation systems, as well as the accumulated production of J. curcas grains and oil. The experiment was conducted in a commercial area in the randomized blocks experimental design with the treatments arranged in a 12 x 2 factorial design, with four repetitions, resulting in 12 treatments with cropping systems and 2 sampling times (February 2012 and May 2012). Soil sampling was performed in February and May 2012, at 0 at 10 cm layer and four composite samples were collected in each cropping system, from five subsamples in each plot. J. curcas intercropping with B. ruziziensis, favors the maintenance of the community of soil microorganisms compared to the treatment with the species P. maximum cv. Massai and Cajanus cajan, which promoted decreasing in soil organic matter dynamics, when compared to the other cropping systems. The monocropping systems of J. curcas and intercropping in rotation systems 2 and 3 achieved higher yields of J. curcas grains and oil over three seasons.