Phytoplankton growth in the Indian Ocean is generally limited by macronutrients (nitrogen: N and phosphorus: P) in the north and by micronutrient (iron: Fe) in the south. Increasing atmospheric deposition of N and dissolved Fe (dFe) into the ocean due to human activities can thus lead to significant responses from both the northern and southern Indian Ocean ecosystems. Previous modeling studies investigated the impacts of anthropogenic nutrient deposition on the ocean, but their results are uncertain due to incomplete representations of the Fe cycling. This study uses a state-of-the-art ocean ecosystem and Fe cycling model to evaluate the transient responses of ocean productivity and carbon uptake in the Indian Ocean, focusing on the centennial time scale. The model includes three major dFe sources and represents an internal Fe cycling modulated by scavenging, desorption, and complexation with multiple, spatially varying ligand classes. Sensitivity simulations show that after a century of anthropogenic deposition, ecosystem responses in the Indian Ocean are not uniform due to a competition between the phytoplankton community. In particular, the competition between diatom, coccolithophore, and picoplankton alters the balance between the organic and carbonate pumps in the Indian Ocean, increasing the carbon uptake along 50°S and the southeastern tropics while decreasing it in the Arabian Sea. Our results reveal the important role of ecosystem dynamics in controlling the sensitivity of carbon fluxes in the Indian Ocean under the impact of anthropogenic nutrient deposition over a centennial timescale.