Particulate organic matter settling out of the euphotic zone is a major sink for atmospheric carbon dioxide and serves as a primary food source to mesopelagic food webs. Degradation of this organic matter encompasses a suite of mechanisms that attenuate flux, including heterotrophic metabolic processes of microbes and metazoans. The relative contributions of microbial and metazoan heterotrophy to flux attenuation, however, have been difficult to determine. We present results of compound specific nitrogen isotope analysis of amino acids of sinking particles from sediment traps and size‐fractionated particles from in situ filtration between the surface and 500 m at Ocean Station Papa, collected during NASA EXPORTS (EXport Processes in the Ocean from RemoTe Sensing). With increasing depth, we observe: (1) that, based on the δ15N values of threonine, fecal pellets dominate the sinking particle flux and that attenuation of downward particle flux occurs largely via disaggregation in the upper mesopelagic; (2) an increasing trophic position of particles in the upper water column, reflecting increasing heterotrophic contributions to the nitrogen pool and the loss of particles via remineralization; and (3) increasing δ15N values of source amino acids in submicron and small (1–6 μm) particles, reflecting microbial particle solubilization. We further employ a Bayesian mixing model to estimate the relative proportions of fecal pellets, phytodetritus, and microbially degraded material in particles and compare these results and our interpretations of flux attenuation mechanisms to other, independent methods used during EXPORTS.