This study reveals the first analyses of the composition and activity of the microbial community of a saline CO2 storage aquifer. Microbial monitoring during CO2 injection has been reported. By using fluorescence in situ hybridisation (FISH), we have shown that the microbial community was strongly influenced by the CO2 injection. Before CO2 arrival, up to 6 × 106 cells ml−1 were detected by DAPI staining at a depth of 647 m below the surface. The microbial community was dominated by the domain Bacteria that represented approximately 60% to 90% of the total cell number, with Proteobacteria and Firmicutes as the most abundant phyla comprising up to 47% and 45% of the entire population, respectively. Both the total cell counts as well as the counts of the specific physiological groups revealed quantitative and qualitative changes after CO2 arrival. Our study revealed temporal outcompetition of sulphate-reducing bacteria by methanogenic archaea. In addition, an enhanced activity of the microbial population after five months CO2 storage indicated that the bacterial community was able to adapt to the extreme conditions of the deep biosphere and to the extreme changes of these atypical conditions.