Agromining aims to rehabilitate contaminated or natural metal-rich soils (ultramafic soils) by extracting metals of high economic importance, such as nickel (Ni), using hyperaccumulator plants and then to recover these metals for industrial purposes. Ultramafic soils are characterized by low fertility levels and this can limit yields of hyperaccumulators and metal phytoextraction. Here, we characterized the potential benefits for phytoextraction efficiency of co-cropping two plants: a Ni-hyperaccumulator (Alyssum murale; Brassicaceae) and a legume (Vicia sativa; Fabaceae). A field experiment with 3 replicates was set up in an ultramafic zone in North West Spain. Four treatments were tested: co-cropping (“Co”), fertilized mono-culture (“FMo”), non-fertilized mono-culture (“NFMo”) and bulk soil (“BS”). “FMo” and “Co” treatments increased the biomass yields of A. murale by 453% and 417% respectively, compared to “NFMo”. “Co” treatment generated 35% and 493% higher Ni-yields than “FMo” and “NFMo”, respectively. Most of the microbial analyses showed that introducing V. sativa (“Co” treatment) into the cropping system had beneficial effects. “Co” treatment significantly modified the phenotypical structure of bacterial communities and raise the relative abundance of the phylum Bacteroidetes and reduced that of Actinobacteria. In addition, non-metric multidimensional scaling analysis of the operational taxonomic units (OTUs) showed that “Co” was clearly separate from all other treatments. Thus, this study showed that co-cropping a hyperaccumulator with a legume in Ni-agromining systems not only improves plant biomass and Ni-yields, but also enhanced some soil microbial enzymatic activities. Ameliorating agromining by replacing fertilizers would combine eco-efficient or sustainable metal recovery with soil fertility/quality improvement.