Brucella species infect animals and also have zoonotic effect. In the present study, risk factors associated with existence of Brucella species in soil were investigated by using metagenomics approach. By using grid based sampling strategy, soil samples (n= 1280) were collected from 256 villages (5 samples/village) of nine districts of Punjab including Lahore, Faisalabad, Sheikhupura, Sargodha, Dera Ghazi Khan, Chakwal, Sahiwal, Gujranwala and Attock. Physical risk factors such as distance near to water irrigation source, distance near to animal market and animal density per village were significantly associated (OR>1) with the prevalence of soil borne Brucella species while other risk factors such as distance from main road and No. of houses per village were less associated (OR<1). Association of chemical risk factors was analyzed by mann-whitney test assuming level of significance of 0.1 and 90% confidence interval. Manganese, lead, zinc, silt, clay, organic matter and soluble salts are significantly associated (P<0.1) with the prevalence of Brucella species while other risk factors including pH, sand, moisture, nitrogen, phosphorus, nickel, cadmium, copper, chromium, iron, calcium, magnesium, sodium and potassium were not associated (P>0.1). In conclusion, physical and chemical risk factors showed association with prevalence of soil borne Brucella species through metagenomics analysis.