Jellyfish play a key role in many pelagic ecosystems, especially in areas of extensive bloom events. In order to understand their role in pelagic food webs and in biogeochemical cycling, the energy stored and the trophic level occupied by jellyfish need to be quantified. To date, the common protocols applied for quantifying jellyfish biomass and analyzing its biochemical composition have been the same as for crustacean zooplankton, despite the difference in the body composition of the 2 groups. With the goal of establishing a uniform and reliable protocol for assessing jellyfish biomass, elemental, stable isotope and amino acid pool composition, we compared several methods commonly used in zooplankton ecology. Our results show that jellyfish dry mass varied with ambient salinity changes, thus giving a poor representation of jellyfish biomass. Moreover, the content of organic matter determined as ash free dry mass was overestimated; it was on average 2.2 times higher when compared to the mass of the retained material after dialysis. Furthermore, we demonstrated that during oven-drying at 60°C the protein-rich jellyfish tissue underwent significant changes: samples were (1) depleted in elemental C and N and total amino acid pool and (2) enriched in 15 N, when compared to freeze-dried samples. We therefore suggest that freeze-drying should be selected over oven-drying before isotope and total amino acid analysis is applied. Overall, the results of this study suggest that the methods used to assess jellyfish biochemical composition should be carefully chosen.