Agromining is a new technology that establishes agricultural systems on ultramafic soils in order to produce valuable metal compounds such as nickel (Ni), with the final aim of restoring a soil's agricultural functions. But ultramafic soils are characterized by low fertility levels, and this can limit yields of hyperaccumulators and metal phytoextraction. The objectives of the present work were to test if the association of a hyperaccumulating plant (Alyssum murale) and a Fabaceae (Vicia sativa var. Prontivesa) could induce changes in physicochemical characteristics of a serpentine soil and in root architecture of a hyperaccumulating plant then lead to efficient agromining practices through soil quality improvement. Based on standard agricultural systems, consisting in the association of legumes and another crop such as wheat or rape, a 3-month rhizobox experiment was carried out to study the effect of the co-cropping (Co) or rotation (Ro) of a hyperaccumulating plant (A. murale) with a legume (Vicia sativa) and incorporating legume biomass to soil, in comparison with mineral fertilization (FMo), on the structure and physicochemical properties of an ultramafic soil and on root architecture. All parameters measured (biomass, C and N contents, and Ni taken up) on A. murale conducted in Co showed the highest values followed by FMo and Ro (Co > FMo > Ro), except for root Ni yield for which Ro was better than FMo. The rhizosphere soil of A. murale in co-cropping had larger soil particles size and better aggregate stability than other treatments. Using geostatistics, co-cropped Alyssum showed a greater root surface area spatial distribution. Moreover, co-cropping and rotation induced lower soil diethylene triamine pentaacetic acid-extractable Ni concentrations than other treatments, but higher pH values. A. murale co-cropped with a legume showed a higher biomass production, improved soil physical characteristics, and enhanced Ni phytoextraction. Consequently, legume introduction in Ni-agromining systems could be an innovative strategy to reduce chemical inputs and to improve soil functions.