In this study, a future projection of marine cold spells (MCSs) over the tropical Indian Ocean is made using a fully coupled regional Earth system model, namely ROM, under two representative concentration pathways (RCPs): RCP4.5 and RCP8.5. In both RCPs, the future MCS properties have been estimated across three distinct time intervals: the near future (NF; 2010–2039), the middle future (MF; 2040–2069), and the far future (FF; 2070–2099). The future MCS computations were examined with respect to fixed historical baseline periods and varying baseline periods. MCSs were frequent, intense, and prolonged during the historical period. ROM effectively simulated these historical MCS metrics and their trends and outperformed the forcing general circulation model as well as the multimodel ensemble mean of Coupled Model Intercomparison Project phase 5 models. In the future, MCSs will cease to occur in ∼13% (4%), ∼56% (66%) and ∼69% (93%) of the area of the tropical Indian Ocean in the NF, MF, and FF respectively under the RCP4.5 (RCP8.5) scenario using a fixed historical baseline period. This departure of MCSs led to the disappearance of events, first identified over the Arabian Sea in both RCPs. The decrease in net heat flux and increase in wind speed contribute to the genesis and severity of MCS events. Further, during the El Niño regime, the MCS events dramatically decrease due to the basin-wide warming, but during the La Niña phase, the MCS intensity and spatial range increase. This study further investigates the sensitivity of MCSs with the choice of baseline period. Adopting varying baseline periods over time does not result in the disappearance of MCSs but does produce declining trends in MCS activity, highlighting the need for careful consideration in choosing a baseline period.