Pakistan experienced profound and accelerating ecological changes resulting from rapid human population growth rate. But, the development syndrome that we are witnessing today, together with the current interest in sustainable development, food production systems and biodiversity conservation bring into focus the soil, which underpins all major developments. Soil processes are important for maintaining normal nutrients cycling in ecosystem including agro- ecosystem. Plant growth rate is dependent on the microbial immobilization and soil food web interaction to mineralize nutrients. In natural ecosystems, the process of immobilization and mineralization are tightly coupled to plant growth but in chemically disturbed systems like crop systems, this coupling may be lost or reduced. Nutrients may be no longer retained within the system. Measuring such disrupted systems of intensive chemical farming may allow determination of a problem long before the sustainability of the farming is altered and the natural production potential is lost leading humans at stake. By monitoring soil organism’s dynamics and detecting detrimental changes in soil profile, crop systems may be saved from further degradation. Thus the present study is aimed at knowing the effects of high input (with use of chemicals) farming on the soil macro-invertebrates among two of the major crops, sugarcane and wheat, in district Faisalabad. Soil samples were collected and soil macroinvertebrates were identified from both crops. Three microhabitats within each crop were sampled to know the effect of phytomorphic heterogeneity on the fauna. Species richness and evenness of the two crop systems was described. The probable role and interactions of various macro-organisms has also been explored.