Amount and characteristics of organic matter pools in key reservoirs within the soil result from microbial activity as impacted by management practices. Their relative abundance with relation to the microbial component of soil can provide indication of change in the soil quality. In the present study a set of soil quality indicators, linked to soil organic matter dynamics, was used in order to evaluate the effects on soil of different management agricultural systems applied to maize crop: conventional, minimum tillage, cultivation in reduced stripe (‘in banda') and protective system. The agronomic trials has started in 1990 and soil samples were collected in 2003 at (0-20) and (20-40) cm depth. Chemical parameters included the determination of total organic carbon, extractable and humified carbon, and related humification parameters. Thermogravimetry (TG) and differential scanning calorimetry (DSC) were also used to characterize labile and recalcitrant fractions of organic matter according to their thermal stability behaviour. Soil microbial resources were investigated through determination of microbial size and activity, i.e. biomass carbon, soil respiration and related parameters (metabolic quotient, potentially mineralizable carbon and kinetic mineralisation rate). Functional diversity of soil microbial community was carried out by CLPP analysis. Investigation results showed that minimum tillage and ‘in banda' systems could be considered as low impacting for soil quality, as increased values of organic carbon were stored in the top soils after more than ten years. Humified fractions, both humic and fulvic acids and humin, were preferentially stored. Thermal characterisation of humic plus fulvic fractions showed that three main pools with different and increasing thermal stability are involved in the thermal breakdown process: similarities between samples of humic plus fulvic acids extracted from conventional and “in banda” plots and from minimum tillage and protective systems, respectively, were observed. In particular, in the first ones the kinetic of thermal oxidation showed the relative prevailing of the more stabilised fractions. Size of pools reacting at lower temperature, resemble cellulosic compounds, were higher in humic and fulvic acids from top soils of protective and minimum tillage system plots, suggesting higher organic matter input and/or less depletion of more mineralisable organic fractions, although differences between sizes of these different thermally reacting pools were not statistically significant. This behaviour agrees with observed lower values of microbial activity kinetic constants, which in turn suggest a faster carbon mineralization in conventional and ‘in banda' plots. Higher amount of microbial biomass was stored in top soils of minimum tillage and ‘in banda' plots, corresponding to higher values of potentially mineralisable carbon at both depths and to higher specific respiration values in the deeper layer, not involved by the tillage system. Different management systems did not significantly impact on metabolic profiles of microbial communities: the main differences were observed between the conventional managing and the others.