Biomarkers are useful tools for assessing the early warning effects of pollutants. However, their responses can be influenced by confounding factors. In this study, we investigated the influence of temperature on multiple biomarkers in the invasive freshwater bivalve Limnoperna fortunei exposed to copper (Cu). The mussels were exposed to low and high environmental Cu concentrations at two temperatures (15 °C and 25 °C). After 96 h, the oxidative stress, neurotoxicity, and metabolic parameters were assessed. Our results showed that temperature is a key factor influencing biomarker responses in mussels, with higher glutathione S-transferase activity and lower energy reserves at cold temperature. In addition, the effects of Cu were greater at the highest concentration at 15 °C (increased lipid peroxidation and cholinesterase activity). Overall, these findings suggest that cold stress increases the susceptibility of L. fortunei to metal effects and highlight the importance of including temperature in toxicity testing and biomonitoring. In addition, using the invasive bivalve L. fortunei as a model could prove valuable in its role as a sentinel species for other organisms.