Nanotechnology holds an immense potential to revolutionize rice production especially in enhancing grain yield. This study evaluates the effect of nanotechnology on grain yield, microbial activity, root development and economic returns over multiple cropping seasons (2022 to 2024). In the 2022 Wet Season (WS), while full-dosed inorganic fertilizer (100 % Rice Crop Manager, RCM) (6.87 tha-1) did not meet the targeted yield due to typhoon-induced lodging, treatments with 50 % RCM combined with Nano fertilizer (NF) produced comparable yields (6.27 to 6.62 tha-1). In 2023 Dry Season (DS), both full RCM and 50 % RCM with NF yielded 6.85 t ha-1; in 2023 WS, 50 % RCM with NF yielded higher yield (4.88 to 5.60 tha-1) than no-fertilizer control (4.35 tha-1); and in 2024 DS, full RCM produced the highest yield of 8.51 tha-1 while 50 % RCM + NF yielded 7.11 tha-1. Soil microbial activity, using Shannon Index was lower in plots with continuous synthetic fertilizer application (H’=2.71) in 2024 DS, showing a decline in soil microbial diversity. Root system development was most robust with full RCM, but the reduced RCM with NF also had favourable root growth, particularly lateral root length. Partial budget analysis revealed that while full RCM provided the highest gross income, the 50 % RCM + NF produced yielded higher net incomes due to lower input costs. The promising results of reduced RCM rates + NF warrant further investigation to assess long-term sustainability, cost-effectiveness and broader environmental impact.