Using observations and long term simulations of an ocean-biogeochemical coupled model, we investigate the biological response in the southern subtropical Indian Ocean (SIO) associated with Ningaloo Niño and Niña events. Ningaloo events have large impact on sea surface temperature (SST) with positive SST anomalies (SSTA) seen off the west coast of Australia in southern SIO during Ningaloo Niño and negative anomalies during Niña events. Our results indicate that during the developing period of Ningaloo Niño, low chlorophyll anomaly appears near the southwest Australian coast concurrently with high SSTA and vice-versa during Niña, which alter the seasonal cycle of biological productivity. The difference in the spatiotemporal response of chlorophyll is due to the southward advection of Leeuwin current during these events. Increased frequency of Ningaloo Niño events associated with cold phase of Pacific Decadal Oscillation (PDO) resulted in anomalous decrease in productivity during Austral summer in the SIO in the recent decades.