As climate change progresses and severe disturbances become routine, understanding rates and mechanisms of recovery in habitat forming species is central to predicting the broader response of ecosystems to climate change. Here, we combined acute experimental heat stress and RNA sequencing to explore patterns of transcriptome plasticity and resilience to heat stress in a common Acropora coral from the World Heritage-listed Ningaloo Reef. Our data showed that corals subjected to sub-bleaching temperatures (33 ºC) elicited a large transcriptional response during heat stress, but quickly recovered to baseline levels of expression 16 hours after temperatures returned to pre-treatment conditions, with no evidence of bleaching. In contrast, corals exposed to a one degree increase (34 ºC) from the sub-bleaching heat treatment, mounted a transcriptional response nearly twice that of the sub-bleaching temperature, showed a lingering stress response in their transcriptome, and eventually bleached. Moreover, variation in the severity of bleaching among colonies was linked to patterns of transcriptome recovery – individuals that bleached heavily showed a larger lag in transcriptional recovery than those with lower levels of bleaching. Together, these findings provide new insight into the genetic mechanisms of heat stress recovery in coral and highlight the role of transcriptional plasticity in the resilience of coral to increasing disturbances.