The Indian monsoon carries large amounts of freshwater to the northern Indian Ocean and modulates the upper ocean structure in terms of upwelling and productivity. Freshwater‐induced stratification in the upper ocean of the Bay of Bengal is linked to the changes in the Indian monsoon. In this study, we test the usefulness of δ¹⁸O and δ¹³C variability records for Globigerina bulloides and Orbulina universa to infer Indian monsoon variability from a sediment core retrieved from the southwestern Bay of Bengal encompassing the last 46 kyr record. Results show that the northeast monsoon was dominant during the Last Glacial Maximum. Remarkable signatures are observed in the δ¹⁸O and δ¹³C records during the Marine Isotope Stage (MIS) 3 to MIS‐1. Our study suggests that Indian monsoon variability is controlled by a complex of factors such as solar insolation, North Atlantic climatic shifts, and coupled ocean–atmospheric variability during the last 46 kyr.