Antibiotics accumulation in aquatic organisms may be of great concern from an ecological point of view but also from a human perspective, especially when they are accumulated in edible animals like marine mussels. In this work, mussels (Mytilus galloprovincialis) were exposed to sulfamethoxazole antibiotic (SMX) at 10 µg/L during 96 h, followed by 24 h of depuration. The experiment was carried out at summer and winter conditions. SMX showed a bioconcentration factor in mussel of 1.5 L/Kg (dry weight) and 69% of the compound was eliminated from the 1 organism in 24 h. The metabolomics approach revealed alterations in amino acids levels (aspartate, phenylalanine, valine and tryptophan) pinpointing disturbances in osmotic regulation and energy metabolism. Besides, the levels of some nucleotides (guanosine and inosine) and a carboxylic acid were also affected. However, SMX exposed mussels did not show any significant alteration in the enzymatic activities related to the xenobiotic metabolism and oxidative stress. Moreover, some of the changes observed in mussel's metabolites suggested alterations in mussel's organoleptic characteristics that can affect its quality as seafood commodity. Overall, our results showed that SMX exposure to marine mussels may have ecological implications by provoking sub-lethal effects to exposed organisms. Nevertheless, no risk for consumers derived from mussel ingestion is expected due to the low bioconcentration capacity of SMX and fast depuration in this seafood type.