The copepod Temora longicornis depends on constant prey availability. Given that climate change may induce food regime shifts, 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 faecal pellet production rates were measured. Carbon (C) and nitrogen (N) budgets were built to investigate differences in dietary C and N partitioning. Copepods fed with nitrogen-depleted diatoms (Diat-), which had the most different C:N ratio to that of T. longicornis, had high metabolic losses and low growth. In contrast, copepods fed with nitrogen-rich dinoflagellates (Dino+) of closer C:N ratio had high metabolic losses, but the highest investment into somatic and reproductive tissue. The results indicate that, under the current climate scenario and nutrient-replete conditions, dinoflagellates are a better food source for T. longicornis. Furthermore, ingestion, respiration, and faecal pellet integrity are adversely affected by low quality food; and egestion is a main pathway in copepods for eliminating excess carbon.