A comparative study of the effect of organic fertilization at different times and doses on soil fertility and crop yield was performed over 3 years in a calcareous loamy soil. Nutrient availability in the soil and macronutrient concentration in leaves and in the edible part of the plants was examined in plots that were previously handled conventionally and ecologically for several years. The organic fertilizers used were manure compost at two doses in plots after 4 years of organic management treatment, and green residues of previous crops in plots with 10 years of organic management. In general, soil organic carbon (C), nitrogen (N), phosphorous (P) and magnesium (Mg) contents were found to be considerably greater in organically fertilized soils in comparison with soil receiving mineral fertilizer (conventional treatment (CT)). For C and N, the highest contents were observed in the long-term organic treatment (OR). However, few differences were found for potassium (K) and sodium (Na). The results obtained for electrical conductivity and pH indicated that, in general, there were no significant differences between treatments. The differences in the values of EC and pH occurred among cultivation cycles irrespective of the type of fertilization, but there was a contradictory trend for each of the above parameters. The results obtained for leaves and the edible part of the plant indicated that, in general, there were no significant differences between treatments, except for P with a trend for higher P content in organic crops. The nitrate values in leaves showed great variability, making it difficult to draw conclusions. The associations of fertilization and the chemical properties of soil with nutrient content in crops were checked by principal component analysis (PCA). For soil data, different clusters were observed between CT and OR treatments. However, PCA showed that the influence of crop type on plant nutrient concentrations was greater than type of fertilization. The effect of fertilization on crop yield was variable depending on plant species. The results indicated that organic fertilization did not cause deficiencies in the nutrient content and yield of vegetables when compared with conventional fertilization, showing that ecological management can be used effectively.