Understanding community assembly and processes driving diversity in deep-sea environments is a major challenge in marine microbial ecology. The deep sea represents the largest ecosystem on Earth, but its remoteness makes the microbial community composition and functionality largely unknown. Moreover, microbial-focused studies comparing different deep-sea habitats like dynamic submarine canyons and slope ecosystems altogether are rare. The present work aims to study the deep-sea seafloor microbial communities (Bacteria and Archaea) of Blanes Canyon and its adjacent western open slope (NW Mediterranean) at ca. 1500 m deep, in autumn and spring, and along the vertical sediment profile. Microbial assemblages were studied in terms of abundance, diversity (a and b), community structure and functional potential through 16S rRNA tag-sequencing to assess their adaptations to the canyon’s idiosyncrasy. Furthermore, the relationships of microbes with environmental variables and a potential predator (nematodes) were also assessed.We observed the microbial assemblages and their predicted functional profiles to be more heterogeneous and with higher temporal variability in the canyon than in the open slope. Although their phyla composition was similar, both the dominant and richest phyla showed significant differences in proportion between canyon and slope. Bacterial diversities were higher in the canyon than in the open slope, together with nematode abundances. Along the vertical sediment profile, microbial abundances consistently decreased with depth in the open slope, while we found more variability within the canyon, linked to an enhancement of aerobic metabolisms in the most superficial sediment layer. Grain size was correlated with microbial abundances and explained part of the variability in the community structure. Nematode and microbial abundances were correlated in slope environments, while in the canyon phytodetritics inputs (Chl a and Chl a: phaeo) and organic carbon seemed to play a role in controlling microbial diversity and abundance. These results suggest that the deep-sea seafloor is strongly connected to coastal and pelagic productive areas through the canyon system in a stronger manner than to the open slope, thus modulating resource availability while driving changes in the microbial biosphere and the higher trophic levels of the deep-sea food web.