The study was initiated to compare crop productivity as affected by a long-term application with homemade liquid fertilizers in leading organic cucumber (Cucumis sativus L.) farms in Suncheon and Kimcheon provinces. A Suncheon farm have applied an EM (effective organism) liquid fertilizer for one year and fifteen years, designating as EM 1-year and EM 15-year plots, respectively, with 4-year and 5-year application of native microbes-liquid fertilizer in Kimcheon farm, designating as Micro 4-year and Micro 5-year plots, respectively. pH in the EM-liquid fertilizer was high to approximately 7.7, and EC in the Micro-liquid fertilizer was 0.1 dS/m higher than those of EM-liquid fertilizer, with similar macro-nutrient concentrations observed in the both liquid fertilizers. Soil EC was the highest to the 10.0 dS/m for the liquid fertilizer with EM 1-year and showed less than 1.5 dS/m for other liquid fertilizer plots. Micro-liquid fertilizer plots had soil OM contents less than 20 g/kg, which was approximately two times less than those of EM plots. Soil microbial properties were not significantly different among the liquid fertilizer plots. SPAD and PS II values were significantly increased by EM 15-year plots with high levels of soil OM and EC. Liquid fertilizer plot with EM 1-year had high concentrations of T-N, Ca, and Na in the cucumber crops but low concentrations of P and Mg, in particular for low K of 1.2% which was two times less than those of desired level for an optimum cucumber growth. The lowest fruit yield was observed for the liquid fertilizer plot with EM 1-year with the highest soil EC accumulated. Liquid fertilizer plot with EM 15-year produced the expanded volume of crop canopy and increased fruit yield. Therefore, long-term of continuous application with an organic liquid fertilizer would have sustainably improved soil stability and the crop productivity.