Conservation agriculture and organic farming are two alternative strategies that aim to improve soil quality and fertility in arable cropping systems through reducing tillage intensity, maintaining soil cover and increasing nutrient recycling, using farmyard and green manures. However, these practices can increase weed infestation or decrease nutrient availability. The objectives of this study were to evaluate the effects of tillage type (mouldboard vs. chisel ploughing), fertilization and green manure on soil parameters (SOC, N, bulk density, carbon stocks, and soil microbial biomass Cmic and Nmic), weed abundance and crop yields in a four-year rotation of spelt, chickpea, winter wheat and lentil in the Mediterranean region (Catalonia, Spain). Tillage and green manure did not affect crop yields or weed biomass, although during the last year of the experiment, plots with mouldboard ploughing had less weed biomass and higher lentil biomass. Fertilization was the most important factor, increasing the cereal yields, SOC, N and soil microbial biomass (Cmic and Nmic) content of the soil. However, fertilization did not favour chickpea and lentil crops because weed competition limited legume crop growth. Overall, there was a loss of SOC and a reduction of carbon stocks over the four years of the trial in the soil because of the deep soil tillage (25 cm) and low crop productivity irrespective of tillage type. In contrast, N content increased in all of the plots and was enhanced by fertilization. The use of chisel plough stratified the distribution of SOC and N in the surface layers (0-10 cm). Both Cmic and Cmic/SOC ratio increased in fertilized treatments, suggesting an increased lability of SOC. The application of more stabilized organic matter may be a better practice to build up soil organic matter and to maintain crop yields in organic farming systems.