In order to characterize spatial patterns and environmental and biological drivers of organic matter remineralization and nutrient regeneration in deep-sea sedimentary habitats, we measured fluxes of nitrate, nitrite, ammonium, phosphate, and silicate at the sediment-water interface during 48-h ex situ incubation of sediment cores. We sampled a total of 6 stations (351–445 m depth) inside the Laurentian Channel Marine Protected Area (MPA), on the outer continental shelf of Newfoundland (Canada). We assessed the potential effect of octocoral sea pens on uni- and multivariate benthic nutrient fluxes at large- and small-scale by comparing sea pen fields and other sedimentary habitats, and cores with and without sea pens. For each station, we evaluated a wide range of environmental variables, including physico-chemical and sedimentary factors, and we identified macrofaunal organisms inhabiting the cores, assessed their taxonomic diversity, community composition, and biological trait expression. Our analysis identified macrofaunal species richness and the density of a few key taxa, as well as environmental factors such as the quantity of sedimentary organic matter as the primary drivers of variation of multivariate benthic fluxes. Macrofauna explained up to 41% of the variation in benthic fluxes, whereas environmental variables only explained up to 19%, highlighting the importance of biodiversity for ecosystem functioning. Uni- and multivariate analysis of fluxes did not reveal clear spatial patterns within the MPA habitats and stations, and fluxes showed high small-scale variability. We found enhanced ammonium efflux rates associated with the presence of sea pens at both small- and large-scale, likely reflecting both direct and indirect effects of these soft corals on organic matter deposition and sedimentary biogeochemical processes. Sea pens, however, did not appear to influence other fluxes, leaving their role for organic matter remineralization unclear. The extreme complexity and small-scale heterogeneity of benthic processes, particularly within what appears to be a relatively homogeneous environment, underscores the need for further studies to facilitate generalizations of patterns and drivers of benthic nutrient fluxes at larger scales, which will ultimately enable the effective integration of ecosystem functioning into conservation strategies.