Although researchers have investigated the impact of Indian Ocean Dipole (IOD) phases on human lives, only a few have examined such impacts on fisheries. In this study, we analyzed the influence of negative (positive) IOD phases on chlorophyll a (Chl-a) concentrations as an indicator of phytoplankton biomass and small pelagic fish production in the eastern Indian Ocean (EIO) off Java. We also conducted field surveys in the EIO off Palabuhanratu Bay at the peak (October) and the end (December) of the 2019 positive IOD phase. Our findings show that the Chl-a concentration had a strong and robust association with the 2016 (2019) negative (positive) IOD phases. The negative (positive) anomalous Chl-a concentration in the EIO off Java associated with the negative (positive) IOD phase induced strong downwelling (upwelling), leading to the preponderant decrease (increase) in small pelagic fish production in the EIO off Java.