We investigate the effect of variable marine biogeochemical light absorption on Indian Ocean sea surface temperature (SST) and how this affects the South Asian climate. In twin experiments with a regional Earth system model, we found that the average SST is lower over most of the domain when variable marine biogeochemical light absorption is taken into account, compared to the reference experiment with a constant light attenuation coefficient equal to 0.06 m−1. The most significant deviations (more than 1 ∘C) in SST are observed in the monsoon season. A considerable cooling of subsurface layers occurs, and the thermocline shifts upward in the experiment with the activated biogeochemical impact. Also, the phytoplankton primary production becomes higher, especially during periods of winter and summer phytoplankton blooms. The effect of altered SST variability on climate was investigated by coupling the ocean models to a regional atmosphere model. We find the largest effects on the amount of precipitation, particularly during the monsoon season. In the Arabian Sea, the reduction of the transport of humidity across the Equator leads to a reduction of the large-scale precipitation in the eastern part of the basin, reinforcing the reduction of the convective precipitation. In the Bay of Bengal, it increases the large-scale precipitation, countering convective precipitation decline. Thus, the key impacts of including the full biogeochemical coupling with corresponding light attenuation, which in turn depends on variable chlorophyll a concentration, include the enhanced phytoplankton primary production, a shallower thermocline, and decreased SST and water temperature in subsurface layers, with cascading effects upon the model ocean physics which further translates into altered atmosphere dynamics.