Seamounts are vulnerable ecosystems targeted by fishing and potentially by future mineral exploitation. Their abundance, widespread distribution, and heterogeneity of faunal and abiotic components require integrated studies at multiscale to describe spatial patterns and identify environmental drivers needed by conservation plans. There is also a lack of knowledge on seamount benthic ecosystems in some regions, such as the Indian Ocean. These gaps, in the context of Marine Protected Areas establishment in the region, have motivated the present study focusing on the Mozambique Channel Eparses islands and flat top seamounts, along a 10-degree latitude gradient. These structures are characterized by complex volcanic and carbonate geomorphologies at multiscale and are distributed along a highly dynamic turbulent ocean circulation area with large anticyclonic eddies. For the first time, we analysed, from seabed image transects obtained by towed-camera on four seamounts, and two volcanic islands - Bassas da India and Mayotte - external slopes, and from multiscale environmental data, how benthic communities respond to this high habitat heterogeneity at regional, and local scales. This study reveals high discrepancies of benthic megafauna richness, density, and beta diversity between seamounts and between slopes of the same islands. Moreover, at similar latitude, seamounts display higher densities than island slopes. The highest densities found on a seamount of the Glorieuses archipelago are explained by strong currents and flat homogeneous geomorphology. Except on this seamount, the beta diversity is high, despite the quite limited depth range explored (84–734 m) and is the highest on island slopes and Hall Bank, driven by the diversity and hardness of the substrate. Beta diversity is mainly due to taxa turnover, with high contribution of the habitat-forming sponges and cnidarians, together with a few mobile taxa. We identified from biogeographic network analysis 12 dominant faunal assemblages, displaying a patchy distribution, with variability in composition both between and within sites. Currents and primary productivity explain ∼15% of the observed assemblage structure along the channel, while geomorphology (km scale), topography (60–500 m scale) and substrate (60-m units) explain together 24% of the faunal spatial patterns. Analysis of spatial structures along island slopes detected some small (100–200 m), medium (∼1 km) and large scale (∼2–6 km) megabenthic community structures, partly explained by topography, substrate, depth, and slope. Despite limited taxonomic identifications for this poorly sampled area, this study reveals an outstanding heterogeneity of megabenthic assemblages at multispatial scales in the Mozambique Channel seamounts and island slopes, in response to the complex hydrography and geology of the area. Further characterization of environmental drivers with greater focus at local scales including hydrographic variables are therefore needed to improve predictions of suitable habitats of vulnerable marine ecosystems.