Soil structure is important for plant growth and ecosystem functioning, and provides habitat for a wide range of soil biota. So far, very few studies directly compared the effects of three main farming practices (conventional, organic and conservation agriculture) on soil structure and soil physical properties. Here, we collected undisturbed soil cores from the FArming System and Tillage long -term field experiment (FAST) near Zurich (Switzerland). This trial compares the effects of conventional tillage, conventional no -tillage, organic tillage and non -inversion reduced tillage under organic farming since 2009. We assessed 28 soil chemical and physical properties and related them to root and microbial biomass as well as to the diversity of bacteria and fungi. Tillage decreased bulk density (-14 %) and penetration resistance (-40 %) compared to no/reduce-tillage, potentially promoting a facilitative environment for plant root growth. Water holding capacity varied among systems, being the lowest in conventional tillage and highest (+10 %) in organic reduced tillage. We observed that microbial biomass and rhizosphere microbial diversity was positively associated with water holding capacity and the occurrence of mesopores. The presence of mesopores could provide additional niche space for microbes possibly explaining its positive effect on microbial diversity. Soil microbial biomass and rhizosphere microbial diversity were higher in plots subjected to soil conservation practices, indicating that tillage has a detrimental effect on soil microbes. Our work demonstrates that organic, conventional and conservation agriculture create contrasting soil physical environments. This work highlights the trade -off between creating a facilitative environment for root growth by tillage and maintaining complex and diverse soil microhabitats for microbes under conservation agriculture.