The possible potential application of Fe-NPs on Fe nutrition, heavy metals uptake and soil microbial community needs to be investigated. In the current research, a pot experiment was used to examine the implications of Fe-NPs (α-Fe2O3 and Fe3O4) on maize growth, Fe uptake and transportation, soil microbial community, and environmental risk. Fe3O4, α-Fe2O3, FeSO4 at a rate of 800 mg Fe kg−1 were applied in soils with four replications under a completely randomized design for a period of 60 days. Results showed that Fe uptake by maize roots were increased by 107–132% than control, with obvious variations across different treatments (Fe3O4> α-Fe2O3> FeSO4> control). Similarly, plant height, leaf surface area, and biomass were increased by 40–64%, 52–91% and 38–109% respectively, with lower values by FeSO4 application. The elevated level of chlorophyll contents and carotenoids and significant effects with control on antioxidant enzymes activities (i.e., catalase, and superoxide dismutase) suggested that application of Fe-NPs improved overall biochemical processes. The differential expression of important Fe transporters (i.e., ZmYS1 and ZmFER1) as compared to control indicated the plant strategic response for efficient uptake and distribution of Fe. Importantly, Fe-NPs reduced the heavy metals uptake (i.e., chromium, cadmium, arsenic, nickel, copper) by complex formation, and showed no toxicity to the soil microbial community. In summary, the application of Fe-NPs can be a promising approach for improving crop productivity and Fe nutrition without negatively affecting soil microbial community, and fostering sustainable agricultural production.