Climate change threatens coral reefs, with recent heatwaves causing widespread coral bleaching and mortality. Soft corals (order Alcyonacea) provide reef structure and habitat, but most reef research has instead focused on reef-building hard corals (order Scleractinia). Reviewing the primary literature documenting the effects of recent (2014–2020) marine heatwaves on corals, a period including the third global coral bleaching event, we found that only 20% (19/94) of studies presented any results of heat stress effects on soft corals, and even fewer (5%) presented taxonomic-specific results, highlighting the need for further study. Using images (n = 6265) collected on 16 expeditions to the world's largest atoll (Kiritimati; central equatorial Pacific) between 2007 and 2019, we quantified soft coral cover around the atoll's shallow (10-12 m depth) forereefs before and after a prolonged heatwave (the 2015/2016 El Niño). Prior to the heatwave, soft coral accounted for 3.0% of the benthic community, with greater cover at more sheltered sites with lower net primary productivity; Lobophytum and Sinularia were the most common genera. We documented a complete loss of soft coral after the heatwave within our sites. New soft corals were detected in 2019, three years after the heatwave. Photos of individual colonies tracked over time revealed that soft coral structures can persist for several years post-mortality, and hard corals can recruit onto these structures. Our study exposes the vulnerability of soft corals to heat stress, which has received scant previous documentation. Future studies examining the effects of heatwaves on coral bleaching and mortality should include soft corals.