In agricultural field, the environmental conditions of soil micro-organisms and their ability to degrade soil organic matter and release nitrogen are strongly modified by the type of tillage. We studied the influence of 4 tillage systems in organic farming on the soil microbial biomass and its potential activities of C and N mineralization. In order to connect soil structure resulting from these tillage systems with the soil microbial biomass and to extrapolate microbial measurements at the field scale, we adopted a particular sampling scheme based on the morphological characterisation of the soil structure by description of soil profiles. We sampled in three layers (0-7, 7-15 and 15-30 cm) clods with distinct physical characteristics: porous clods with visible porosity (tau clods) and compacted clods without visible porosity (delta clods). On each clod we measured distinct physico-chemical (C and N content, C/N, pH and total porosity) and microbiological characteristics (soil microbial biomass SMB, C and Nmin). This sampling method revealed the influence of soil structure and organic matter repartition on SMB and its activity and allowed a more precise assessment of tillage managements on the soil microbial functioning during the transition period from ploughing to no ploughing.