To investigate the efficiency of effective microorganisms (EM), organic and inorganic fertilizers combinations on agronomic and quality traits of onion and spinach, the present study was carried out at Faculty of Agriculture, Gomal University during 2009- 10 and 2010-11. A series of experiments were conducted using various available materials like pressmud (sugar mills waste), farm yard manure, compost, and poultry manure with or without EM. Inorganic fertilizers like NPK were also included in the trails treatments with half and full recommended doses. Integrated use of organic wastes especially pressmud and inorganic fertilizers co-applied with EM caused positive impact on the nutrient levels of spinach and onion harvested soil. Moreover, both in spinach and onion all the physiological parameters were significantly improved where pressmud was applied during both years experiments. Nutritive quality of spinach and onion was also significantly improved. Results indicated that pressmud with EM was more effective in enhancing growth, yield and quality of both vegetables (spinach and onion) and improved the soil physico-chemical characteristics. Farm yard manure, compost and poultry manures also showed encouraging results and improved the crop growth, yield and quality and soil properties. Adding NPK to the pressmud along with EM was found to be the most desired combination. The study suggested to apply organic wastes along with readily available chemical fertilizers (NPK) and EM to minimize the risk of reduced plant growth.