Agromining describes the technique of growing plants to “mine” metals present in naturally enriched or contaminated soils. This technique comprises a series of processes including improvement of soil quality and production of biomass in order to obtain metals from the ash of harvested hyperaccumulators, which can be considered bio-ore. The aim of this study was to evaluate different agronomic practices for Ni agromining of the hyperaccumulator species Odontarrhena chalcidica by analyzing (i) Ni yields and (ii) parameters related to soil fertility, biodiversity, and Ni availability. We tested various types of fertilizers including farmyard manure and assessed cultivation of the hyperaccumulator in either continuous monoculture or cropping in rotation with the legume Vicia ervilia. A 2-year field experiment was established on typical ultramafic Vertisols in eastern Albania. The current study presents the results obtained in the second year of cultivation. After 2 years of agromining, fertilization with animal manure or rotation with the legume improved several soil properties and increased the yield of phytoextracted Ni by four and five times, respectively, relative to non-fertilized plots. The fertilization treatments did not affect the bacterial diversity indexes but significantly impacted the bacterial community structure. We suggest a fertilization regime including the application of pig or chicken manure (at doses equivalent to NPK 260:105:260; 260:390:260, respectively) every 2 years or the implementation of crop rotation with legumes as effective strategies for developing Ni agromining on Vertisols.