To evaluate the soil properties and judge the balance sheet of nutrients as influenced by different maize (Zea mays L.) genotypes grown under organic production system in sub-humid southern plain and Aravalli hills zone of Rajasthan, a two-year field experimentation was undertaken during Kharif 2015 & 2016 at Instructional Farm (Organic Farming Unit), Rajasthan College of Agriculture, Udaipur, Rajasthan. The experiment comprises twelve genotypes of maize (PQPM -1, PM -9, PHM -3, Sugar – 75, Madhula, Misty, PM-5, PM-3, VL Amber Pop corn, Amber Popcorn, Navjot and Farmers selection). The experiment was laid out in a randomized block design with three replications. Result showed that maize genotype i.e. Navjot observed with highest net gain of available N (55.83 kg ha-1) and available K (85.83 kg ha-1) in soil. Net available P was found negative (-0.085 to -13.11 kg ha-1) in all the varieties of maize except variety PM-5 (3.62 kg ha-1). Response of different maize varieties with respect bulk density, particle density, pH, EC, CFU (Bacteria, Fungi and Actinomycetes) and dehydrogenase enzyme activity were found non-significant. The water use efficiency was found significantly higher under genotype Farmers Selection of maize and it was stayed statistically at par with variety Navjot genotype. According to prevailing cropping system, early cultivars PHM-3and PM-3 and medium duration PM-3, PQPM-1, PM-5 and Novjot genotypes of maize can be promoted for organic cultivation of production in given area of Sub-Humid Southern Plain and Aravalli Hills Region of Rajasthan.