There is a need to simultaneously preserve evidence of interactions between the biological community and soil structural properties of a soil in as near an intact (natural) state as possible. Three dehydration techniques were implemented and assessed for their ability to minimise disruption of both biological and physical properties of the same arable soil sample. Dehydration techniques applied until samples were at constant weight were i) air-drying at 20 °C (AD); ii) −80 °C freeze for 24 h, followed by freeze-drying (−80FD); and iii) liquid nitrogen snap freeze, followed by freeze-drying (LNFD) and were compared to a moist control. Physical structure was determined and quantifled in three dimensions using X-ray computed tomography and microbial phenotypic community composition was assessed using phospholipid fatty acid (PLFA) proflling. This study conflrms that any form of dehydration, when preparing soil for simultaneous biological and physical analysis, will alter the soil physical properties, and cause some change in apparent community structure. Freeze-drying (both the LNFD and −80FD treatments) was found to minimise disruption (when compared to the moist control soil) to both the soil physical properties and the community structure and is a preferable technique to air-drying which markedly alters the size and character of the pore network, as well as the phenotypic proflle. The LNFD was the preferred treatment over the −80FD treatment as samples show low variability between replicates and a fast turn-around time between samples. Therefore snap freezing in liquid nitrogen, followed by freeze drying is the most appropriate form of dehydration when two sets of data, both physical and biological, need to be preserved simultaneously from a soil core.