Up to one-third of all described marine species occur in coral reefs, but the future of these hyperdiverse ecosystems is insecure due to local and global threats, such as overfishing, eutrophication, ocean warming and acidification. Although these impacts are expected to have a net detrimental effect on reefs, some organisms, like soft corals, may remain unaffected or benefit from anthropogenically induced environmental change, replacing stony corals in future reefs. Despite their importance as future ecosystem engineers, the molecular mechanisms leading to the resilience to anthropogenic-induced stress observed in soft corals remain unknown. Here, we use manipulative experiments, proteomics, and transcriptomics to show that the molecular toolkit used by Pinnigorgia flava, a common indo-pacific gorgonian, to deposit its calcium-carbonate skeleton is resilient under simulated climate change. Sublethal, simulated global warming triggered a stress response in P. flava but did not affect the expression of the 28 transcripts encoding Skeletal Organic Matrix (SOM) proteins present in this species' skeleton. Exposure to simulated ocean acidification did not cause a stress response but triggered the downregulation of many transcripts, including an osteonidogen homolog present in the SOM. The observed transcriptional decoupling of the skeletogenic and stress-response toolkits provides a mechanistic explanation for the resilience to anthropogenically-driven environmental change observed in soft corals.