The copepod Temora longicornis depends on constant prey availability, but its performance also depends on how efficiently it utilizes its food sources. Our research goal was to understand copepod energy allocation in relation to diet quality. The working hypothesis was that Temora performs better on the diet whose elemental ratio is closest to its own. Diatoms (Diat) and dinoflagellates (Dino) cultured in nutrient-replete (+) and nitrogen-depleted (-) conditions were fed to the copepods. Ingestion, respiration, excretion and egg and fecal pellet production rates were measured. Carbon (C) and nitrogen (N) budgets were built to investigate differences in dietary C and N partitioning. Copepods fed nitrogen-depleted diatoms (Diat-), which had the most different C:N ratio to that of Temora longicornis, had high metabolic losses and low growth. Copepods fed nitrogen-rich dinoflagellates (Dino+) with a more similar C:N ratio to their own also had high metabolic losses, but displayed the highest investment into somatic growth and egg production. The results indicate that dinoflagellates are a better food source for T. longicornis. Furthermore, consumption of low-quality food leads to higher respiration rates and faster leakage of dissolved organic carbon from copepod fecal pellets; and egestion is a main pathway in copepods for eliminating unabsorbed and non-metabolized carbon.