Protothaca thaca is an important bivalve species inhabiting the upwelling ecosystem of Chile and Peru. Temperature in this ecosystem changes dramatically during El Niño (EN) events, with P. thaca showing high tolerance to increased temperatures. To understand the metabolic processes behind this adaptation we studied the effects of temperature on standard metabolism, growth and body condition index of P. thaca from Northern Chile. Oxygen consumption, daily growth rate and body condition index of animals acclimated to 12, 16 and 20°C were measured using an intermittent flow-through system. Our results show that these processes are significantly lower at 12°C compared to 16 and 20°C. No differences are observed between the higher temperatures. The relative thermal independence of routine metabolism is suggested to conserve energy, which allows the species to be more tolerant to high temperatures. Overall, the physiological responses of P. thaca at whole-animal level largely confirm that this clam is well suited to tolerate positive thermal anomalies associated with strong EN in the study area. However, results at lower temperatures show contrasting responses, which emphasizes the need to be cautious in sclerochronological studies, which tend to assume direct relationships between single environmental factors and micro-growth increment width.