Pre-planting reductive soil disinfestation (RSD) has been shown to restructure soil microbial communities and suppress soil-borne diseases. However, the effect of RSD on soil chemical and microbial characteristics in different cropping systems has not been studied. We sampled rhizosphere soils of Salvia miltiorrhiza, a staple medicinal plant in China, from three cropping system: continuous cropping monoculture, rotation cropping monoculture with Platycodon grandiflorus, and intercropped with Paeonia lactiflora. In a pot experiment, rice straw was applied as amendment to these soils before irrigating to saturation and covering with plastic film to simulate RSD. Soil chemical and microbial properties, mycorrhizal colonization, were determined using chemical analyses and high-throughput sequencing, and the growth of seedlings of S. miltiorrhiza was evaluated. RSD significantly improved soil chemical properties, changed the microbial community composition and structure, increased microbial diversity, and facilitated seedling growth. The efficacy of RSD differed greatly among the three cropping systems. RSD performed better in rotation soils compared to the soils from continuous cropping and intercropping. RSD markedly decreased the relative abundance of pathogenic Fusarium genus in intercropping soils only. In conclusion, the effectiveness of RSD should be evaluated in the context of a specific cropping system.