Abstract Heat accumulation and rising sea surface temperatures (SST) are currently major stressors for coral reefs worldwide. Coral reefs are also impacted by cool SST anomalies, although the dynamics of cold stress events are less well understood. Here, we estimate coral bleaching metrics in the Indonesian Seas using a high‐spatial‐temporal‐resolution SST data set. We reveal that cold stress events caused by positive Indian Ocean Dipole (IOD) events tend to be more intense and longer‐lasting than heat stress events. Although these events are currently not intensifying, extreme cold stress reaches magnitudes comparable to the most extreme heat stress events recorded to date. In the Indonesian Seas, heat stress events caused by El Niño have become more frequent in recent years. When followed by a negative IOD event, heat stress events are prolonged and more severe. However, reefs in Karimata and Makassar Straits are protected from heat/cold stress, offering potential thermal refugia.