With the advancement of present-day ocean color satellites, the spatiotemporal variations of oceanic Chlorophyll-a (Chl-a) concentration, a proxy for phytoplankton population, can be monitored at regional and global scales. Estimating long-term changes in Chl-a concentration, however, is mainly constrained by the limited availability of ocean color data and the significant influence of climate oscillations like the El Niño Southern Oscillation (ENSO). In this study, we investigate the influence of ENSO on regional and global Chl-a timeseries using two ocean color datasets spanning from September 1997 to December 2022. Our analysis found that global Chl-a concentration exhibits a significant increasing trend over the study period. Most of the increasing trends are detected in the Southern Hemisphere (SH) and high-latitudinal regions, including the Southern Ocean. In light-limited regions like the Southern Ocean, enhanced Chl-a concentration shows a strong positive correlation with warming sea surface temperature (SST). Conversely, most oceans in the Northern Hemisphere (NH) exhibit decreasing trends, which are highly correlated with warming SST and ENSO phases. Additionally, we identify distinctive fingerprints of four extreme ENSO events: two extreme El Niño events (1997–1998 and 2015–2016) and two triple La Niña events (1998–2001 and 2020–2022) in these timeseries. Furthermore, empirical orthogonal function (EOF) analysis reveals that the dominant mode of interannual Chl-a variability is associated with an ENSO-like pattern, accounting for about 13 % of the total variability. Intriguingly, this principal mode is highly correlated with the phases of ENSO (R = -0.87) and Pacific Decadal Oscillation (PDO) (R = −0.90) on an interannual scale. This study provides insights into assessing the impacts of ENSO on long-term Chl-a trend estimation.