Abstract To improve soil fertility, efforts need to be made to increase soil organic matter content. Conventional farming practice generally leads to a reduction of soil organic matter. This study compared inorganic and organic fertilisers in a crop rotation system over two cultivation cycles: first crop broad bean ( Vicia faba L.) and second crop mixed cropped melon-water melon ( Cucumis melo-Citrullus vulgaris) under semi-arid conditions. Total organic carbon (TOC), Kjeldahl-N, available-P, microbial biomass C (Cmic), and N (Nmic), soil respiration and enzymatic activities (protease, urease, and alkaline phosphatase) were determined in soils between the fourth and sixth year of management comparison. The metabolic quotient (qCO 2), the Cmic/Nmic ratio, and the Cmic/TOC ratio were also calculated. Organic management resulted in significant increases in TOC and Kjeldahl-N, available-P, soil respiration, microbial biomass, and enzymatic activities compared with those found under conventional management. Crop yield was greater from organic than conventional fertilizer. The qCO 2 showed a progressive increase for both treatments during the study, although qCO 2 was greater with conventional than organic fertilizer. In both treatments, an increase in the Cmic/Nmic ratio from first to second crop cycle was observed, indicating a change in the microbial populations. Biochemical properties were positively correlated ( p < 0.01) with TOC and nutrient content. These results indicated that organic management positively affected soil organic matter content, thus improving soil quality and productivity.