The soil fertility depends on the maintenance of microbial processes and activities for the completion of nutrient cycles. The management practices of soil and man-made activities which add contaminants i.e., heavy metals in the soil potentially have long term effects over microbial diversity in different ecosystems like in current study (Agriculture research Centre, the soil near industrial area and rural area). The present PhD program has examined the effects of heavy metals over microbial biomass, soil respiration and metabolic quotient in the said areas. An experiment was carried out in Agriculture Research Centre at Bahauddin Zakariya University, Multan on the effect of heavy metals on soil microbial biomass, soil respiration and metabolic quotient during four seasons. Microbial biomass showed significance in all three metals during spring and winter at (P<0.001) while in case of soil respiration only Cd showed significance in both seasons. Metabolic quotient expressed significance at (P<0.001) in case of Cu+Cd during spring and with Zn+Cd at (P<0.001) in winter season. The results show that metals are in sequence of Cd>Cu>Zn in their effects and toxicity and spring is dominant in case of all metals. The soil was verified for soil physical and chemical contamination nearby Multan Industrial Estate (MIE). Six parameters consisting of pH, Organic Matter (OM%), Zn, Cu, Cd and Pb were taken as representatives for the study from five sites out of which the farthest two sites were chosen as control. Physico-chemical parameters were determined by using standard techniques Plasma Spectrophotometer. The results showed significant relationship among parameters at (P<0.05, P<0.01 and P<0.001). First two sites near industrial area expressed high level of contamination of metals. The distribution of trace metals was observed in order of Zn> Pb> Cu> Cd which explains that out of four elements, Zn and Pb contributed prominent level of absorption in the soil. The final results of the overall study conclude that microbial diversity and soil diversity are interdependent and both can augment each other. However, rural and urban soils are dissimilar from each other in both containing soil microbial community and physiochemical properties and rural soil has more clear support for microbial community than in urban soil. Moreover, industries are the contributing factor of heavy metal contamination. It is suggested such practices should be ceased at the earliest that increased the level of soil pollution.