The effects of cassava mill effluent impacted rhizosphere soil on heterogenous physiological groups of soil microorganisms, and the phytochemical of the leguminous plants were evaluated using standard microbiological and biochemical techniques. The results revealed that the fungal isolates across the (0%-100%) polluted plots were Saccharomyces sp., Mucor indicus, Fusarium sp. and Gliocladium sp. while the bacterial isolates were Chromobacterium sp., Corynebacterium sp., Bacillus sp., Acinetobacter sp. and Escherichia coli. The nitrogen-fixing bacterial isolates were Azotobacter sp., Azospirillum sp., Frankia sp., Bradyrhizobium sp., Hebasspirillum sp., Cyanobacteria and Anabaena sp. The microbial loads in the simulated soil phyto-remediated with Centrosema pubescence fluctuated across the concentration gradient with no significant difference (p>0.05 ANOVA) while that phyto-remediated with Calopogonium mucunoides showed a decline in bacterial and nitrogen fixing bacteria population and an increase in fungal population. There were no significant differences (p>0.05 ANOVA) in the microbial population. Cassava mills effluent also affected the phytochemical and proximate composition of the leguminous plants used for the simulation experiment with no significant difference (p>0.05 ANOVA). Relevant legislation on environmental sustainability and plant protection should therefore be put in place to protect plants and autochthonous microbial community for man’s biotechnological exploitation.