We evaluated the effect of 4000 mg zinc oxide (ZnO, 99%, 30 nm) nanoparticle on the physicochemical and microbiological properties of organic manure amended ultisol and loam soil cultivated with Arachis hypogaea using standard methods. The results indicate varying effects on the physicochemical properties in relation to the soil type. The pH of the control ultisol at 7.85 ± 0.17 and 8.3 ± 0.12 in the amended ultisol whereas, the control loam was 7.15 ± 0.17 and 7.41 ± 0.11 in the amended soil indicating 1.06- and 1.04-times higher difference than the controls respectively. Phosphorus concentration at 57.82 ± 0.54%, 50.81 ± 0.22% and 55.97 ± 0.04%, 59.97 ± 0.02% was 1.14 times lower in the ZnO amended ultisol and 1.07 times higher in amended loam soil compared to the respective controls. The organic matter content in the control and amended ultisol was 2.28 ± 0.32% and 0.91 ± 0.02%, 3.68 ± 0.36% and 0.36 ± 0.02% in the control and amended loam soil. The concentration of nitrate in the control ultisol was 0.05 ± 0.01% and 0.03 ± 0.01% in the amended soil. The nitrate in the control loam soil was 0.08 ± 0.01% relative to 0.02 ± 0.01% in the treated soil and these differences were significant at p = 0.05. The concentration of nutritive salts was reduced and in contrast iron, copper, exchangeable acids, exchange capacity, clay and silt increased in the amended soils. Further to this, heterotrophic ammonia and nitrate-oxidizing bacterial population were inhibited in the amended soils and denitrifying organisms were stimulated. The organisms were members of the genera Pseudomonas, Xanthobacter, Enterobacter, Bacillus, Lactobacillus, Citrobacter, Nitrosomonas, Agromyces and Rhizobium. ZnO nanoparticles altered the soil physicochemical properties which exacerbated the negative effect on microbial abundance and varied with the soil type.