There is increasing evidence that insecticidal transgenic crops can indirectly cause detrimental effects on arthropod predators or parasitoids when they prey on or parasitize sublethally affected herbivores. Our studies revealed that Chrysoperla carnea is negatively affected when fed Bt-susceptible but not Cry1Ac-resistant Helicoverpa armigera larvae that had fed Bt-transgenic cotton expressing Cry1Ac. This despite the fact that the predators ingested 3.5 times more Cry1Ac when consuming the resistant caterpillars. In order to detect potential differences in the nutrient composition of prey larvae, we evaluated the glycogen and lipid content plus the sugar and free amino acid content and composition of caterpillars fed non-Bt and Bt cotton. The only change in susceptible H. armigera larvae attributable to Bt cotton feeding were changes in sugar concentration and composition. In case of the Cry1Ac-resistant H. armigera strain, feeding on Bt cotton resulted in a reduced glycogen content in the caterpillars. The predators, however, appeared to compensate for the reduced carbohydrate content of the prey by increasing biomass uptake which caused an excess intake of the other analyzed nutritional compounds. Our study clearly proves that nutritional prey-quality factors other then the Bt protein underlie the observed negative effects when C. carnea larvae are fed with Bt cotton-fed prey. Possible factors were an altered sugar composition or fitness costs associated with the excess intake of other nutrients.