<p>Soft corals are significant members of the reef ecosystem, and their existence is threatened by extensive anthropogenic activities and the associated climate change. In this context, <i>Sinularia</i> species were collected from different locations across the Egyptian Red Sea coast with varying environmental conditions (i.e., Hurghada and Marsa Alam), to comprehensively explore their metabolic response to stress, and to identify markers of their resilience to environmental stressors. Untargeted metabolomics encompassing GC-MS (gas chromatography-mass spectrometry) and UPLC-HRMSMS (ultra-high-performance liquid chromatography coupled to high-resolution mass spectrometry) were employed to explore the respective changes in their primary and secondary metabolome. The recorded metabolome reflected the stressful and competitive environmental conditions existing in Hurghada despite the lower sea temperature. <i>Sinularia</i> samples collected from Hurghada showed higher levels of glycerol and free amino acids in addition to cembranes and hydroxylated steroids, <i>versus</i> higher total amino acid content in Marsa Alam samples. Glycerol is linked to stress in corals, acting as an energy reserve and mediating homeostasis, while free amino acids act as osmolytes in stressed organisms. In contrast, total amino acid content reflects active protein synthesis, metabolic flexibility, and sufficient nutritional resources. This study underscores how metabolomics can provide holistic insights into the biochemical adaptations of corals, enabling a deeper understanding of how climate change and human-induced stressors reshape reef health at the molecular level. Observed biochemical changes highlight that coral reefs are greatly affected by the escalating human activities, which significantly contribute to the degradation of marine habitats, posing a severe threat to coral ecosystems.</p>