As bentonite hosts a diverse spectrum of indigenous microorganisms with the potential to influence the long-term stability of deep geological repositories, it is essential to understand the factors determining microbial activity under repository conditions. Here, we focus on two such factors, temperature and swelling pressure, using a suspension of Cerny Vrch bentonite to boost microbial activity and visualise microbial response. Suspensions were exposed to differing pressures (10–15 MPa; simulating the effect of swelling pressure) and temperatures (60–90°C), followed by a period of anaerobic incubation at atmospheric pressure/laboratory temperature to assess microbial recovery. Microbial load and community structure were estimated using molecular-genetic methods, with presence of living cells confirmed through microscopic analysis. Pressure application had no influence on overall microbial activity or proliferation, proving that pressure evolution during bentonite swelling is not the key factor responsible for microbial suppression in saturated compacted bentonites. However, pressure treatment did cause significant shifts in microbial community structure. We also demonstrated that microbial activity decreased with increasing temperature, and that heat treatment strongly influenced bentonite microbial community structure, with several thermophilic taxa identified. A temperature of 90°C proved to be limiting for microbial activity and proliferation in all bentonite suspensions.