Coral Sr/Ca records have been widely used to reconstruct and understand past sea surface temperature (SST) variability in the tropical Pacific. However, in the eastern equatorial Pacific, coral growth conditions are marginal, and strong El Niño events have led to high mortality, limiting opportunities for coral Sr/Ca‐based SST reconstructions. In this study, we present two ∼25‐year Sr/Ca and Mg/Ca records measured on modern Porites lobata from Wolf and Darwin Islands in the northern Galápagos. In these records, we confirm the well‐established relationship between Sr/Ca and SST and investigate the impact of heat stress on this relationship. We demonstrate a weakened relationship between Sr/Ca and SST after a major (Degree Heating Months 9°C‐months) heat stress event during the 1997–1998 El Niño, with a larger response in the Wolf core. However, removing data that covers the 1997–1998 El Niño from calibration does not improve reconstruction statistics. Nevertheless, we find that excluding data after the 1997–1998 El Niño event from the calibration reduces the SST reconstruction error slightly. These results confirm that coral Sr/Ca is a reliable SST proxy in this region, although it can respond adversely to unusual heat stress. We suggest that noise in Sr/Ca‐SST calibrations may be reduced by removing data immediately following large heat extremes.