Bacteria control the “life” in soil inner space via various biological processes. Their immediate environment can be influenced by abiotic microenvironmental factors. Thus, we hypothesize that variations in soil structure, texture, and moisture status can both be affected by and control bacterial activity and diversity. A multi-disciplinary approach was made by linking soil physics with biology to discover the biophysical interactions.   Soil was sampled from a Danish agricultural field (Silstrup, Denmark) with opposing gradients in clay and organic matter. Soil texture, organic carbon, bulk density, water retention, air-filled pore space, gas diffusivity, and air permeability were measured. Simultaneously, microbial population composition and microbial diversity at the sampling locations were determined using next-generation sequencing technology, particularly using 454 deep amplicon sequencing. It was observed that bacterial diversity had significant and positive correlation with soil clay content, bulk density, and water-filled pore space. It also had significant but negative correlation with soil organic carbon, silt content, volumetric water content, and soil-water matric potential. Furthermore bacterial species distribution followed the patterns of water retention and gas transport properties, reflected by soil structure indices. The results clearly indicate that soil structural constituents control microbial diversity, having major impact on the variations of biophysical microenvironments for soil microbes.