Twenty-six soil samples were collected from 13 paired orchards (organically vs. conventionally managed) homogeneous for age, rootstock and cultivars, belonging to the Eastern Sicily Organic Citrus farm Network. The soil quality was evaluated by chemical and biochemical indicators. The total organic C, humification parameters and isoelectric focusing of extracted organic matter were measured to quantify the size of relevant soil C pools. In addition, C turnover was evaluated by determining microbial C mineralization, C microbial biomass and by calculating the mineralization and metabolic quotient (qCO2). The results obtained demonstrated that organic citrus soils were characterized by a general increase in all the organic matter pools, which means a greater C supply for soil metabolic processes. This observed trend did not directly influence the organic matter turnover, indicating that the organic approach could act as a soil C-sink. The soil microflora of organically managed soils showed an improved efficiency in use of energy and organic resources, corresponding to an increased ability of soils under organic management to sustain biological productivity in the long term.