The Boom Clay layer in Belgium is investigated in the context of subsurface nuclear waste storage, making use of the underground laboratory HADES. The HADES facility offers a rather unique access to a subsurface microbial community, in an environment of which all geological and geochemical characteristics are being thoroughly studied. This study presents the first elaborate description of a subsurface clay microbial community, residing in Boom Clay borehole water. Using an integrated approach of microscopy, metagenomics, activity screening and cultivation, the presence and activity of this community is disclosed. Despite the low energy environment, the microscopy and molecular analyses show a surprisingly large bacterial diversity and richness, tending to correlate positively with the organic matter content of the environment. Among different samples, a core bacterial community comprising seven bacterial phyla is defined, including both aerobic and anaerobic genera with a range of metabolic preferences. In addition, when using the appropriate media, a considerably large fraction of this community is found cultivable, active in situ and matching the metagenomic data. In conclusion, this study shows the possibility of a microbial community of relative complexity to actively persist in subsurface Boom Clay.