The Pacific oyster Crassostrea gigas is a sessile animal that undergoes highly dynamic and stressful environmental constraints all along its life in the intertidal zone and estuaries. We analyzed the physiological effects induced by low environmental concentrations of two pesticides, metconazole (0.2 and 2 µg L-1) or isoproturon (0.1 and 1 µg L-1), or in mix (0.2 and 0.1 µg L-1 respectively) known to be encountered by oysters in the field. At such trace-level, metconazole and isoproturon induced a metabolic stress, reflected by an important over-activation of the sensing-kinase AMP-activated kinase  (AMPK). Such deregulation reflect alteration of energy management, since the sensing-molecule AMPK plays a key role in C. gigas energetic metabolism, as well as alteration in the adaptation to environmental stress, given its role in hypoxia. Neither pesticide had any effect on eco-physiological parameters during the 14 days-experiment: filtration rate, food consumption, growth, and available energy reserves remained unchanged. In contrast, using two-dimensional electrophoresis, we identified changes in proteins that belong to energetic metabolism and cytoskeletal induced by metconazole or isoproturon. Analyses of antioxidant enzymes revealed an increase in oxidative stress pathway in superoxide dismutase and catalase in some conditions. Taken together, our results proved that trace-level environmental concentrations of metconazole or isoproturon provoke important deleterious effects at the biochemical level in oyster, by inducing a metabolic stress and oxidative stress response. Such alterations were not directly reflected at the level of the whole organism when measuring eco-physiological parameters. Identifying the impacts of pesticides at environmental concentrations using biochemical approaches is thus a promising field of research to improve monitoring processes.