The observed decline in microbial abundance with increasing depth has been associated to various environmental factors. Meanwhile, the role of geometrical constraints and soil-bacteria mechanical interactions remains poorly analyzed. Pore and pore-throat sizes may restrict habitable pore space and traversable interconnected porosity, and sediment-cell interaction may cause puncture or tensile failure of the cell membrane. In this study we compile published evidence on the presence of bacteria in deep sediments as well as pore and pore-throat size data in sediments at different depths to establish possible geometrical conditions for the sediment-cell complex. Compiled data are complemented with experimental results gathered through controlled axial compression experiments that reproduce the mechanical consolidation of deep sediment sequences. Then, we analyze the mechanical interaction between bacteria and sediments that may cause cell death. Finally, we combine data and model predictions to define the main regions in a particle-size versus depth space that characterize the fate of bacteria: “active and motile,” “trapped inside pores,” and “dead or dormant.” These regions constrain hypotheses related to the role of biological activity in deep sediments, research protocols and sampling methods, the viability of bioremediation strategies for contaminated sites, and the potential development of bioengineered sediments.