Menez Gwen, Lucky Strike, and Rainbow are the three most visited and well-known deep-sea hydrothermal vent fields in the Azores region, located in the Mid-Atlantic Ridge. Their distinct geological and ecological features allow them to support a diversity of vent communities, which are largely dependent on Bacteria and Archaea capable of anaerobic or microaerophilic metabolism. These communities play important ecological roles through autotrophy, feeding, and in establishing symbiotic associations. However, the occurrence and distribution of these microbes remain poorly understood, especially in deep-sea sediments. Here we provide the first comparative survey of the sediment-associated microbial communities from these three neighboring vent fields. The taxonomic profiles of bacterial, archaeal and eukaryotic representatives were assessed by rRNA gene tag pyrosequencing. The Menez Gwen, Lucky Strike, and Rainbow studied sites presented distinct microbiomes. The occurrence of anaerobic methanogens and microaerobic Epsilonproteobacteria, particularly at the Menez Gwen site, suggest that the sediment communities are potentially enriched in subseafloor microbes, rather than from pelagic microbial taxa. Cosmopolitan OTUs were also detected mostly at Lucky Strike and Rainbow sites and affiliated with the bacterial clades JTB255, Sh765B-TzT-29, Rhodospirillaceae and OCS155 marine group and with the archaeal Marine Group I. Some variations in the community composition along the sediment depth were revealed. Trace metal contents and hydrothermal influence are suggested as being reflected in the composition of the microbial assemblages in the sediments of the three vent fields. Altogether, these findings represent valuable information for the understanding of the microbial distribution and potential ecological roles in deep-sea hydrothermal fields.