Copepod fecal pellets (FPs) are an important but highly variable component of the global Biological Carbon Pump (BCP). This study decoupled and quantified how copepod grazing and prokaryotic activities affect BCP efficiency under different phytoplankton dietary regimes. With a diet of diatoms, copepods FP production rates double, FP sinking rates triple, and FP decomposition rates are significantly lower relative to those with dinoflagellate diets. When diatoms are the primary producers, these biological activities synergistically enhance the efficiency of FP exports to the deep ocean. Opportunistic particle-attached (PA) prokaryotes were crucial to FP decomposition. Metagenomic analyses revealed that CAZymes and lysosomal enzyme abundances correlated with FP decomposition rates. These functional enzymes targeting phytoplankton- and copepod intestine-derived macromolecules from the PA prokaryotic communities were key to FP decomposition. Genomic properties of the Planctomycetota revealed that strong motile ability, detoxification systems and macromolecule degradation enzymes enabled the success of these opportunistic PA prokaryotes. Elevated temperatures amplified FP decomposition rates by enhancing enzyme abundances, and especially accelerated the decomposition of FPs composed of dinoflagellates. This reduced BCP efficiency, as rapidly recycled organic materials will remain in surface waters. Our findings highlight the synergistic biological activities amplifying the effects of phytoplankton composition changes on BCP efficiency. This underscores the importance of considering grazing regimes in combination with microbial dynamics in assessing ocean carbon cycling.