Zooplankton carcasses are common within aquatic systems and potentially serve as organic-rich substrates for bacteria. We compared the microbial decomposition of representative crustacean (copepod) and non-crustacean (rotifer) zooplankton carcasses and monitored changes in carcass protein and lipid contents. Our results showed that carcass decomposition was mainly driven by bacteria colonizing from the surrounding water. Carcass-associated bacteria displayed higher protease and lipase activities than free-living bacteria. Protein content of copepod carcasses decreased by 70% within the first 8 h and shifted from larger to smaller sized proteins, while protein loss in rotifer carcasses was insignificant. Carcass lipid content did not change significantly over 24 h in either zooplankton type, although polar branched fatty acids increased on copepod carcasses indicating an increase in viable microbial biomass. Our results suggest differential turnover of protein versus lipid within a zooplankton carcass and that carcasses from different zooplankton groups would affect water column microbial processes differently.