Increasing consciousness about future sustainable agriculture and hazard free food production has lead organic farming to be a globally emerging alternative farm practice. We investigated the accumulation of air-borne heavy metals in edible parts of vegetables and in cultivated soil horizon in organic farming system in a low rain fall tropical region of India. The factorial design of whole experiment consisted of six vegetable crops (tomato, egg plant, spinach, amaranthus, carrot and radish) x two treatments (organic farming in open field and organic farming in glasshouse (OFG)) x seven independent harvest of each crop. The results indicated that except for Pb, atmospheric deposition of heavy metals increased consistently on time scale. Concentrations of heavy metals in cultivated soil horizon and in edible parts of open field grown vegetables increased over time and were significantly higher than those recorded in OFG plots. Increased contents of heavy metals in open field altered soil porosity, bulk density, water holding capacity, microbial biomass carbon, substrate-induced respiration, alkaline phosphatase and fluorescein diacetate hydrolytic activities. Vegetable concentrations of heavy metal appeared in the order Zn > Pb > Cu > Ni > Cd and were maximum in leaves (spinach and amaranths) followed by fruits (tomato and egg plant) and minimum in roots (carrot and radish). Multiple regression analysis indicated that the major contribution of most heavy metals to vegetable leaves was from atmosphere. For roots however, soil appeared to be equally important. The study suggests that if the present trend of atmospheric deposition is continued, it will lead to a destabilizing effect on this sustainable agricultural practice and will increase the dietary intake of toxic metals.