Synchronous effects of biochar on heavy metals stress, microbial activity and nodulation process in the soil are rarely addressed. This work studied the effects, under greenhouse conditions, of selected heavy metals Cd2+, Pb2+ and Ni2+ on soybean plants grown in two different soils amended with biochar, and studied their effect on the microbial and enzymatic activity. As a result of the interference between heavy metals and biochar, biochar overcame heavy metal problems and maintained a microbial population of major groups (bacteria−fungi). There was an increase in the degree of resistance (RS) of the major microbial groups to heavy metals when biochar was added to the soil under study. Numbers of bacterial nodules significantly increased, particularly by using the higher rate of biochar compared to the control, either by adding biochar alone or by mixing it with the selected heavy metals. The arginase activity was increased by 25.5% and 37.1% in clay and sandy soil, respectively, compared to the control. For urease (UR), the activity was increased by 105% and 83.8% in clay and sandy soil, respectively, compared to the control. As a result, considerations of using biochar as a soil amendment should be first priority.