The flexible regulation of feeding behaviour and nutrient metabolism is a prerequisite for consumers to grow and survive under variable food conditions. Thus, it is essential to understand the ecological trade-offs that restrict regulatory mechanisms in consumers to evaluate the consequences of nutrient limitations for trophic interactions. Here, we assessed behavioural and physiological adjustments to nutrient deficiencies in copepods and examined whether energy limitation, food digestibility or co-limitation with a second nutrient restricted compensatory mechanisms. A combination of 13C-labelling and compound-specific stable isotope measurements revealed that copepods compensated nitrogen deficiencies by raising retention efficiencies of amino acids (AA). The costs of higher retention efficiencies were reflected in the doubling of structural fatty acids (FA), probably required for morphological adaptations of the gut. A depletion of highly unsaturated FA in storage lipids and their selective retention suggested that these FA became co-limiting and restricted a further increase in AA retention efficiencies. Copepods feeding on phosphorus-limited algae showed a marked increase in ingestion rates but were not fully able to compensate dietary deficiencies. The increase in ingestion rates was thereby not restricted by higher foraging costs because energy storage in copepods increased. Instead, thicker cell walls of nutrient-limited algae indicated that algal digestion resistance restricted the extent of surplus feeding. The strongly nutrient-specific response of copepods had large implications for recycling rates, growth efficiencies and the potential top-down control at the plant–animal interface. Compensatory mechanisms to mitigate nutrient deficiencies are therefore an essential aspect of trophic interactions and have the potential to alter the structure of food web. A plain language summary is available for this article.@en