Tillage modifies soil structure and crop residue distribution and in turn affects the ability of soil micro-organisms to degrade soil organic matter and release nutrients for crop growth. In organic farming, soil microbiological activity is of primary importance as nutrient supply is mainly dependent on the degradation of soil organic matter by soil micro-organisms. The aim of this work was therefore to study, in organic farming, the effects of four tillage systems [mouldboard ploughing (MP), shallow mouldboard ploughing (SMP), reduced tillage (RT) and shallow soil tillage (ST)] on soil structure, soil microbial biomass (SMB) and its potential activity (Cmin) during the first year following the treatments. To study simultaneously the effects of soil structure modifications and crop residue distribution on SMB and Cmin, we adopted a sampling scheme based on a morphological description of soil profiles. We distinguished and sampled compacted and non-compacted clods (Δ and Γ clods) at three depths (0–5, 5–15 and 15–30 cm). This method enabled us to have a precise estimation of the effects of tillage treatments on SMB and Cmin. MP reduced compacted zones and limited unfavourable conditions for microbial growth and enabled a homogenous distribution of SMB in the soil profile. At the opposite, the ST increased compacted zones in the soil profile and limited SMB development below the top few centimetres. The SMP and the RT systems appeared as intermediate techniques. RT seemed to be a conservation tillage technique which could be used in organic farming.