Due to the ever-increasing worldwide plantation of sweet leaf Stevia rebaudiana (Bertoni), how to efficiently and effectively utilize the huge amounts of leaf residues that contain abundant nutrients after sweetener extraction becomes an eminent issue. One option is to return these residues into soil, as organic manure in the fresh or composted form, in order to both sustain soil fertility and avoid potential environmental pollution. In a field experiment, we studied if the Stevia leaf residue returning affected both plant and soil microbial growths as well as the possible change of soil microbial community composition. In doing so, four treatments were employed: (1) no chemical fertilization and no Stevia residue returning (no-fertilization control); (2) chemical N, P, and K fertilization (NPK); (3) fresh Stevia residue plus NPK (FS + NPK); and (4) composted Stevia residue plus NPK (CS + NPK). Responses of plant and soil microbial communities to Stevia residue input after 1-year fertilizations were investigated by multiple approaches, including soil enzyme assay, real-time quantitative polymerase chain reaction, and PCR-denaturing gradient gel electrophoresis. Our results showed that compared to the sole NPK and no-fertilization control, returning Stevia residues to soil stimulated the enzyme activities of dehydrogenase, invertase, and urease, except neutral phosphomonoesterase; thereby, both the Stevia leaf biomass and sweet glycoside of rebaudioside A were increased. The soil microbial community abundance was increased by the returning of Stevia residues, and their composition was shifted, evidenced by an increase of relative abundance of some genotypic groups, such as Bacillales. Further molecular analysis of Bacillus confirmed that this guild composition was positively influenced by Stevia residue returning, especially for Bacillaceae. Our results demonstrated an effective use of Stevia residues as organic manure for promoting Stevia yield and quality through stimulating soil microbial growth and enzyme activities. © 2013 Springer-Verlag Berlin Heidelberg.