Bone waste utilization in agriculture can be achieved through pyrolysis. The potentiality of bone-derived biochar as a soil conditioner and its effects on the soil bacterial community structure and composition in multi-metal contaminated mining soils have not yet been explored. Therefore, cow bone (CB) was used as biochar feedstock and pyrolyzed at low (500 °C; CBL) and high (800 °C; CBH) pyrolytic temperature with an application rate of 0 (control), 2.5, 5, and 10%, w/w, dosages. Then, the untreated and treated soil was incubated and cultivated by maize in the greenhouse. The response of soil microbial communities, function, enzyme activity and plant health attributes were analyzed after maize harvesting. The results revealed that nutrient-rich biochar (CB) enhanced the content of total nitrogen (up to 26%), total phosphorus, (up to 27%), and dissolved organic carbon (up to 74%), in the soil. The CB application revealed significant shifts in the bacterial both at phylum and a class level. At the phylum level, it has been noticed that a high dose of CB (10%) caused contrasting effects on the Proteobacteria diversity both at low and high pyrolytic temperature having reverse effects. The CBL-10 at a higher dose (10%) enhanced the Actinobacteria (65%), Parcubacteria (138%), and Firmicutes (48%) community while CBH-10 favors the Acidobacteria (11%) and Proteobacteria (12%) microbial community. The CBH enhanced the β-glucosidase (51%) and alkaline phosphatase activities (71%) at the lower doses (2.5–5%) as compared to control, while the activities of these enzymes decreased with the higher application doses. However, the activity of dehydrogenase significantly decreased (77%), particularly with CBH. We conclude that CBL applied at 2.5-5% dose found suitable in terms, can be utilized as a potential soil amendment in Zn and Cd contaminated soils since it improves soil microbial abundance, function, enzyme activity, and plant growth.