Oceanic Net primary production (NPP) results from the photosynthesis of marine plankton, which accounts for half of the global primary production and influences the carbon cycle, and transfers organic matter and energy to marine ecosystems. Anthropogenic activities severely stress the ocean ecosystem through warming and acidification and have significantly altered NPP. In this context, we assess the long-term changes in NPP in the Indian Ocean (IO) with respect to the changes in physical processes and nutrient input to the oceans. Under the extreme warming scenario, the western AS shows a positive trend (0.7–0.9 °C/yr) in summer, where the basin-wide seasonal maximum in NPP is observed (400–500 mg/m3). Similarly, the rise in SST and decline in DNO3 in the upwelling-prone regions like western AS, Seychelles-Chagos Thermocline Ridge (SCTR), and southwest AS have adversely affected the NPP in IO. Contrary to this, cooling is observed in the northern AS during winter (-0.1–0.2 °C/yr), combined with the rise in DFe concentration, favour the NPP there. A decline in NPP in the IO (-25.31 mg/yr) will adversely affect the marine food chain and biogeochemical cycles.