Summary We explored how marine dissolved organic matter ( DOM ) altered by bacterial growth and protozoan grazing modify the metabolism of Southeastern Cantabrian Sea ( CS ) and NW M editerranean Sea ( MS ) coastal bacterial communities. Major metabolic features were measured in treatments with half of the natural water replaced by water with different DOM quality, characterized by fluorescent DOM analysis and collected from key times of the predator–prey curve. In both ecosystems, protozoan-altered DOM led to similar increases in bacterial carbon demand (238% and 213%) and decreases in bacterial growth efficiency ( BGE : 56% for the CS and 46% for the MS ). These low BGEs were caused by similar bacterial production but much higher bacterial respiration rates, which in turn were positively related to aminopeptidase activity. However, in the CS bacterial community dominated by Bacteroidetes (41%), the enhanced hydrolytic activity was produced at a lower metabolic cost than in the MS , dominated by SAR 11 (47%), which suggests a better adaptation of Bacteroidetes to the DOM altered during protozoan grazing. These results highlight protozoan grazing as a relevant factor influencing BGE in coastal ecosystems, and relate bacterial community composition to the major metabolic processes that result after a change in the quality of marine DOM .