Most of the research dedicated to agromining has focused on cultivating a single hyperaccumulator plant, although plant diversity has been shown to positively modify soil characteristics. Hence, we compared the effect of cropping a nickel-hyperaccumulator Alyssum murale with a legume (Vicia sativa) to A. murale's mono-culture, on the bacterial diversity and physico-chemical characteristics of an ultramafic soil. A pot experiment with 5 replicates was conducted in controlled conditions for 11 months. The treatments studied were: co-cropping and rotation vs. mineral fertilization controls and bare soil. The introduction of legumes induced a clearly positive effect on the soil's microbial biomass carbon and nitrogen. Arylsulfatase and urease activities tended to be enhanced in the co-cropping and rotation treatments and to be lessened in the mineral fertilization treatments. However, β-glucosidase and phosphatase activities were seen to decrease when legumes were used. Our results showed that the rotation treatment induced a higher organic matter content than the fertilized control did. Actinobacteria was the most-represented bacterial phyla and had lower relative abundance in treatments associating legumes. Conversely, the relative abundance of Acidobacteria and Gemmatimonadetes phyla increased but not significantly in treatments with legumes. The relative abundance of Chloroflexi phylum was shown to be significantly higher for the fertilized rotation control. The relative abundance of β-Proteobacteria subphylum increased but not significantly in treatments with legumes. NMDS analysis showed a clear separation between planted treatments and bare soil and between co-cropping and rotation and fertilized controls. Shannon index showed reduction in microbial diversity that was mainly due to chemical inputs in the soil. This study showed that these new cropping systems influenced both the bacterial diversity and the physico-chemical characteristics of an ultramafic soil. In addition, this study provides evidence that mineral fertilization can negatively impact bacterial communities and some of their functions linked to biogeochemical cycles.