During the last 4 decades punctual occurrences of extreme ocean temperatures, known as marine heatwaves (MHWs), have been regularly disrupting the coastal ecosystem of the Peru-Chile eastern boundary upwelling system. In fact, this coastal system and biodiversity hot-spot is regularly impacted by El Niño events, whose variability has been related to the longest and most intense MHWs in the world ocean. However the intensively studied El Niños tend to overshadow the MHWs of shorter duration that are significantly more common in the region. Using sea surface temperature data from 1982 to 2019 we investigate the characteristics and evolution of MHWs, distinguishing events by duration. Results show that long duration MHWs (> 100 days) preferentially affect the coastal domain north of 15° S and have decreased in both occurrence and intensity in the last four decades. On the other hand, shorter events, which represent more than 90% of all the observed MHWs, are more common south of 15° S and show an increase in their thermal impact as well as on the number of affected days, particularly those spanning 30–100 days. We also show that long duration MHWs variability in the coastal domain is well correlated with the remote equatorial variability while the onset of short events (< 10 days) generally goes along with a relaxation of the local coastal wind