The coupling relationship between biogenic deposits and productivity may vary across different stages or regions. To explore the responses of biogenic deposits to productivity since the last glacial period, we analyzed multiproxy biogenic deposit data from Core YDY09 in the Bay of Bengal (BoB) spanning the past 30 ka. We first observed that the trends of biogenic depositional records (radiolarians, BSi, and CaCO3) were in antiphase to that of the productivity of siliceous organisms in the overlying waters during the Last Glacial Maximum (LGM), Heinrich Stadial 1 (HS1) and late deglacial period (LdGp; 15–10 ka) in the northeastern Indian Ocean. We suggest that productivity variations were influenced mainly by the Indian summer monsoon (ISM) during the last deglaciation to glaciation. The decoupling between high productivity and low biogenic deposition during the LGM and LdGp was attributable to significant dilution by large-scale terrigenous inputs. Unlike the substantial inputs of terrestrial materials caused by low sea levels during the LGM period, the sea level rose rapidly during the LdGp period, suggesting that the intense ISM may have played a crucial role at that time. Conversely, the high amount of biogenic deposition during HS1 could be attributed to weak terrigenous dilution resulting from diminished rainfall in the Intertropical Convergence Zone (ITCZ). The strong terrigenous dilution observed during the LGM and weak terrigenous dilution during the HS1 in the BoB were consistent with findings in the northern South China Sea (SCS), except the unique LdGp period. Our findings will enhance the understanding of the decoupling mechanisms between biogenic deposits and productivity in global marginal seas.