Safflower is one of the most important oilseed crops in semi-arid regions. The soil of semi-arid areas often encounters micronutrient deficiencies. However, nutrients imbalance seems to affect the quantitative and qualitative aspects of the oil as well as plant growth. Current experiment was carried out to evaluate the impact of different application practices (soil application and foliar spray) of micronutrients (Fe, Zn, Mn) on oil content, fatty acid profile and yield components of safflower under full and limited irrigations. Results showed that all of investigated traits were significantly affected by fertilizer treatment and irrigation system. The highest seed protein content was recorded for plants grown by soil application of Zn under limited irrigation condition. The highest oil content was achieved by soil application of Zn under full irrigation condition. The water deficit significantly reduced some qualitative characteristics such as oleic acid, palmitic aid, stearic acid, linoleic acid, iodine value and saponification value. The highest head number per plant, seed number per head and seed yield recorded in plants grown by soil application of Fe and Zn under full irrigation condition. Although the use of micronutrients improved qualitative characteristics in comparison with control, the best qualitative characteristics were achieved with the soil application of Zn and Fe. The elimination of micronutrient deficiencies and the balanced supply of nutrients through soil along with optimal and timely irrigation can significantly increase the efficiency of safflower production systems and improve the quality of the oil.