Due to various anthropogenic activities like industrial processes, vehicular emissions and use of inorganic fertilizers as well as pesticides, the presence, distribution and assimilation of soil contaminants is inevitable. Therefore, the regular monitoring of different ecosystems viz., air, water and soil is mandatory. Considering the harmful consequences of soil pollution on health of living systems, the present work was planned to estimate the physicochemical parameters, protein and lipid content and genotoxic potential employing Allium cepa root chromosomal aberration assay following in situ and root dip treatment methods in agricultural soil samples under cultivation of wheat and rice collected from five different zones of Amritsar city. The present study reveals the presence of different physicochemical alterations in agricultural soil samples of Amritsar (India). The genotoxic response in Allium cepa test system further creates an alarm to the health of farmers as well as the consumers of different food crops/fruits/vegetables.