This study uses the Coupled Model Intercomparison Project phase 6 (CMIP6) Earth System Model simulated outputs and satellite-based chlorophyll-a (Chl-a) observations to understand the changes in Chl-a concentration in the recent past and its future changes in the Indian Ocean. Based on the availability of common models across the three future scenarios (SSP5-8.5, SSP2-4.5, and SSP1-2.6), we chose 11 CMIP6 models for this study. The climatology of these model-simulated historical outputs is assessed against a satellite-based Ocean Colour Climate Change Initiative-Version 5 (OC-CCI-V5) data product. The Indian Ocean (IO) is divided into four regions (Arabian Sea (AS), Bay of Bengal (BoB), Central Indian Ocean (CIO), and Southern Indian Ocean (SIO)), and the performance of each of these CMIP6 models are evaluated in each of these regions of IO. Based on the statistical analysis, GFDL-ESM4 is found to be the best-performing model across all four IO regions. However, the GFDL-ESM4 underestimates Chl-a concentration in the AS and CIO regions ( 0.07 mg/m), whereas it overestimates Chl-a concentration in the BoB region ( −0.07 mg/m). The GFDL-ESM4 performs relatively better in the SIO region with a less biased Chl-a concentration. Under the SSP5-8.5 scenario, the future changes of Chl-a indicate a large decrease in the Chl-a concentrations ( −0.04 mg/m) in the western coast of the AS, the western coast of BoB, and the southern Java coast. This large decrease in Chl-a concentration is limited to nearly 0.01 mg/m under the SSP1-2.6 scenario. Therefore, the implementation of extreme mitigation measures can control the reduction of surface Chl-a concentration in the IO. The analysis to understand future changes in Chl-a concentration in the mixed layer of six upwelling zones in the IO indicates a decrease in Chl-a concentration in the mixed layer by −0.06 to −0.09 mg/m in all future scenarios.