Increasing anthropogenic CO2 concentration in the atmosphere is altering sea water carbonate chemistry with unknown biological and ecological consequences. Whereas some reports are beginning to emerge on the effects of ocean acidification (OA) on fish, very little is known about the impact of OA on jellyfish. In particular, the benthic stages of metagenetic species are virtually unstudied in this context despite their obvious importance for bloom dynamics. Hence, we conducted tri-trophic food chain experiments using the algae Rhodomonas salina as the primary producer, the copepod Acartia tonsa as the primary consumer and the benthic life stage of the scyphozoans Cyanea capillata and Chrysaora hysoscella as secondary consumers. Two experiments were conducted examining the effects of different levels of CO2 and food quality (experiment 1) and the effect of food quality and quantity (experiment 2) on the growth and respiration of scyphozoan polyps. Polyp growth and carbon content (µg polyp−1) were not affected by the CO2 treatments, but were significantly negatively affected by P limitation of the food in C. capillata but not in Ch. hysoscella. Growth and carbon content were reduced in low-food treatments, but increased with decreasing P limitation in high- and low-food treatments in C. capillata. Respiration was not significantly influenced by food quality and quantity in C. capillata. We conclude that phosphorus can be a limiting factor affecting the fitness of scyphopolyps and that P-limited food is of poor nutritional quality. Furthermore, OA, at least using realistic end-of-century scenarios, will have no direct effect on the growth of scyphistomae.