Fecal pellets (FP) are a key component of the biological carbon pump, as they can, under some circumstances, efficiently transfer carbon to depth. Like other forms of particulate organic carbon (POC), they can be remineralized in the ocean interior (particularly in the upper 200 m), or alternatively they can be preserved in the sediments. The controls on the attenuation of FP flux with depth are not fully understood, in particular, the relative contributions of zooplankton fragmentation and microbial/zooplankton respiration to FP loss. Collection of sinking particles using Marine Snow Catchers at three ecologically contrasting sites in the Scotia Sea, Antarctica, revealed large differences in POC flux composition (5–96% FP) and flux attenuation despite similar temperatures. To determine the importance of microbial respiration on FP loss in the upper mesopelagic, we made the first ever measurements of small scale oxygen gradients through the boundary layer at the interface of krill FP collected from the Scotia Sea. Estimated carbon-specific respiration rates of microbes within FP (0.010–0.065 d−1) were too low to account for the observed large decreases in FP flux over the upper 200 m. Therefore, the observed rapid declines in downward FP flux in the upper mesopelagic are more likely to be caused by zooplankton, through coprophagy, coprorhexy, and coprochaly. Microbial respiration is likely to be more important in regions of higher temperatures, and at times of the year, or in depths of the ocean, where zooplankton abundances are low and therefore grazing and fragmentation processes are reduced.