The paper aimed to present the relationships between soil microbial biomass content and the sizes of soil structural aggregates in the leached chernozem from central part of Moldova in three different lands management systems as the long-term arable chernozem with crop rotation without fertilizers, long-term arable land covered for nine years with cover crops (grass mixture ryegrass and lucerne) which are used each year as a green manure and chernozem under 60 year-old fallow. It is based on the research carried out in the experimental sites of “Nicolae Dimo” Institute of Pedology, Agrochemistry and Soil Protection from village Ivancea, Orhei District. The data have been processed into the following indicators: soil structure, organic carbon content, microbial biomass carbon. Carried out research show that fallow chernozem under the forest stripe has a significantly better structure than arable and phyto improved soils. In all three experimental sites carbon content have a uniform distribution regardless of the aggregates size. Microbial biomass carbon is concentrated in the smallest aggregates of fallow cernozem in the surface layer and has a polynomial distribution in below layer. Arable cernozem is characterized by fairly uniform distribution in all size soil aggregates but with a slightly higher concentration in the 0.5-0.25 mm aggregates. Phyto improved cernozem differs from the arable by microbial biomass carbon higher content in medium sized (the highest in 3-2 mm) aggregates in the first layer from the surface. As a conclusion, despite a uniform organic carbon distribution in different sized soil aggregates, microbial biomass carbon has some preferences due to the used agricultural practice and can be an indicator of soil health.