Value of the data •Detailed proteomic dataset of gilthead sea bream livers in fish exposed to low temperature during growth; •Differential protein abundances between the two temperature phases: Cooling phase (t0-t1, from 18 °C to 11 °C) and Cold Maintenance phase (t1-t2, at 11 °C) are useful to understand the dynamics and metabolic shifts occurring in sea bream liver with decreasing water temperature; •Shotgun proteomics dataset improves previous data on fish hepatic metabolism during cold exposure; •The proteomic dataset might be advantageous to other research groups working on the development of feeds designed to compensate the thermal stress encountered by fish in offshore farming conditions.