The repeated addition of organic materials to the soil greatly affects the physical, chemical and biological characteristics. In the present work, we analyzed changes in soil quality properties of the tilled layer caused by different agronomic managements of maize which supply different amounts of carbon (C) and nitrogen (N) through the addition of slurry, farmyard manure or plant residues. The agronomic history of the analyzed soils, which derived from a medium-term (11 y) field experiment located in NW Italy, represents typical managements of maize for this region. The area is characterized by highly intensive agriculture, with consequent risks to soil degradation that could be limited by the efficient utilization of organic inputs and by recycling within cropping systems, the large amounts of manure that are produced from the many animal breeding farms in this region. We used a combination of both different chemical (soil organic C and total N) and biochemical indicators (potential soil respiration, potentially mineralizable N (PMN) and potential soil microbial biomass (SMB)). We considered the suitability of the selected biochemical indicators to describe the changes in soil characteristics resulting from the past management. The results showed that the application of the different organic materials, in addition to urea-N fertilizer, increased SOM contents and altered the selected soil biochemical properties compared with the unfertilized treatment, especially in the upper 15 cm of the 0-30 cm tilled soil layer. Farmyard manure applications caused the greatest increase in SOM content, PMN and potential SMB, whilst return of maize straw produced the largest increase in potential soil respiration, but had less effect on total soil organic C and SMB. The use of slurry only caused a moderate increase in SOM and showed intermediate changes in biochemical properties. Also, the rate of C accumulation in the soil per unit of C applied was higher for farmyard manure application than for slurry and straw incorporation in the soil. Fertilization with only mineral N did not induce an increase in Corg and Ntot and even reduces soil N mineralization potential. Because of the high variability in the data, potential SMB carbon could be considered as a less successful indicator for differentiating between past agronomic histories and effects on soil quality, whilst microbial activity (measured by potential soil respiration) and PMN, gave a more reliable and useful indication of the amount of easily decomposable organic carbon.