Conventional agriculture that uses extensive tillage without organic inputs to soils can cause a degradation in soil quality. The improvement of soil organic matter (SOM) content can be achieved through the use of organic amendments. Application of organic amendments, such as compost, is a reliable tool to improve soil quality. On-farm composting is an ecological technology and can be used to recycle agricultural waste materials, such as animal manure or crop residues, that can be incorporated into the soil to improve soil quality. Therefore, the objective of this work was to characterize, by CPMAS-NMR spectroscopy and chemical properties, a commercial organic waste compost and an on-farm compost and, then, to compare their use as organic amendments on soil quality. A greenhouse study on intensive agricultural soils of Southern Italy was done. The following amendments, as soil treatment, were used: a municipal compost (MC), with C:N 13.3, and an on-farm compost (OF), with C:N 17.1, applied at the rate of 8.5 and 6.0 Mg DMha−1, respectively. After one, four, eight, twelve and fifteen months soil samples were collected and analyzed for chemical (pH, electrical conductivity, limestone, CEC, available phosphorus, organic carbon, total nitrogen and exchangeable bases) and microbial (urease, phosphomonoesterase, β-glucosidase, total hydrolytic activity and Biolog Ecoplate™) properties. MC compost was characterized by larger electrical conductivity and exchangeable Na+ content with respect to OF compost, while this latter was characterized by about twice of organic carbon (470gkg−1). As showed by CPMAS-NMR spectroscopy, OF compost was characterized not only by cellulosic polysaccharides, but also significant amounts of both alkyl components and lignin derivatives. An effective increase of soil organic carbon (SOC) in plots under MC (+36%) and OF (+25%) composts, respectively, was reached at the end of the experiment. Soil amendments improved soil biological functions as revealed by a general trend of positive effects on hydrolase activity, phosphomonoesterase, β-glucosidase as well as urease. EC and exchangeable Na+ were considerably larger only in the plots under MC compost (25% and 19%, respectively), with respect to control plot. The possible increase of soil salinity after compost amendment may negatively affect soil quality in the long-term. In conclusion, our results demonstrated that the supply of compost produced on-farm, can enhance soil biological and biochemical properties, without the drawbacks of municipal composts, representing a promising alternative to the latter and an important way to reuse wastes produced by cultivation and processing of vegetables.