Global warming is one of the major causes of reef coral ecosystems’ degradation. Predictions of further rise in sea surface temperatures call for urgent action. In this study, a holistic method for bio-monitoring heat stress in reef ecosystems was tested and optimized. Long-term induction of antioxidant enzymes and oxidative stress by elevated temperatures (30 °C and 32 °C) was assessed on fragments of reef-building corals and compared to control conditions (26 °C). The quantification of both oxidative stress, through lipid peroxidation (LPO) levels, and antioxidant enzyme activities: superoxide dismutase (SOD), catalase (CAT), and glutathione S-transferase (GST) in a long-term experiment (60 days), using seven Indo-Pacific reef-building coral species, provided useful information that was interpreted in combination with the observed partial mortality and growth rate of these organisms. These biomarkers were combined in integrated biomarker response (IBR) indices, either in an antioxidant defense mechanisms and oxidative stress response category (approach A: GST, CAT, LPO, and SOD) or in an integrated stress response category – organism performance (approach B: GST, CAT, LPO, SOD, partial mortality, and growth rate). The results of this study indicate that the IBRs were responsive to temperature treatment and dependent on the coral species. The approach B was the most adequate since it better reflected the stress suffered by the tested species, whereas the set of four biochemical biomarkers (approach A) was not enough to explain the organismal response of most of the tested species to thermal stress conditions.