Understanding the environment and the biogeochemistry that occurs in the deep subsurface is of major importance in order to improve processes of geological resources exploitation (i.e. oil and gas fields, geothermal and water resources, mining). The microorganisms, namely bacteria and proteobacteria, are involved in both positive and negative effects concerning those processes. Because of their activity, they can induce changes in the liquid phases composition (e.g. souring effect, oils maturation) as well as in the solid phases by precipitating new minerals (biomineralization) or dissolving others (biodissolution, biocorrosion). The appearance of biofilms is also a source of local chemical gradients, microenvironments and plugging. One of the major hindrance to the study of the biogeochemistry in deep subsurface is the difficulty to keep samples under subsurface conditions for their analysis or, at least, to suppress the chemical and biological shifts due to degassing. On the other side, recent developments in the engineering of microchips and microfluidic has allowed to mimic subsurface conditions in terms of temperature, pressure, mineral and pore space environment. Besides, chips can now be used for direct observations. In this study, we have developed a system of percolation under high pressures (100 bars) in such conditions and provided new possibilities to make direct and non-destructive observations of the microbial deep communities by using vital stain with spectrophotometric and microscopic approaches. These applications as well as the corresponding first observations will be presented and discussed.