The extremotolerant bacterium Deinococcus radiodurans is used as a model to explore the limits of life on Earth and beyond. In experiments performed in an ultra-high vacuum chamber with a vacuum ultraviolet (VUV) synchrotron beamline, this microorganism was exposed to conditions present on an extraterrestrial environment unprotected by an atmosphere, such as outside a spacecraft or on an asteroid, relevant in the context of planetary protection and panspermia hypothesis. Different methods were used to obtain the biologically relevant information from this investigation. Counting of colony forming units, the traditional approach for viability assessment, is limited to measuring the survival of the cells. For a more in-depth study of damage mechanisms at subcellular levels, specific molecular probes (propidium iodide and dihydrorhodamine 123) were applied and whole populations could be analysed, cell by cell, by flow cytometry. VUV radiation caused a substantial loss of viability, though only a fraction of the cells presented membrane damages even at the largest tested fluences. Additionally, intracellular oxidative stress was also detected upon exposure. These results point to significant VUV inactivating effects extending beyond the cells' outermost structures, in contrast to a more superficial role that could be expected due to the highly interacting nature of this radiation range. Nevertheless, it was observed that microscopic-level shading sufficed to allow the persistence of a small surviving subpopulation for the longer expositions. This study contributes to unveiling the response of biological systems under space conditions, assessing not just cell viability but also the mechanisms that lead to inactivation.