This study was conducted to investigate the differences in the proximate composition (moisture, fat, protein and ash), cholesterol content, energy, mineral composition (Na, Ca, Mg, K, P, Fe and Zn) and fatty acid profile of rainbow trout, Oncorhynchus mykiss, after frying, boiling, or microwaving. Results showed that all cooking methods reduced moisture and increased total protein, fat and ash contents. Also all minerals increased significantly during the microwave and frying methods. Statistical results showed that the major fatty acids among the saturated and monounsaturated fatty acids in each fish were palmitic (C16:0) and oleic (C18:1) acids, respectively. In addition, linoleic acid (C18:2) was predominant in the n-6 polyunsaturated fatty acids (PUFA) in both cooked and raw trout. The EPA (eicosapentaenoic acid; C20:5 ω3) and DHA (docosahexaenoic acid; C22:6 ω6) acids were the major fatty acids among total n-3 acids in fish samples. The fatty acids profile of the cooked fish showed a saturated (SFA) and monounsaturated (MUFA) decrease and an increase in PUFA contents. However, the ω-3 fatty acids content increased in microwaved samples but decreased in the fried samples. Moreover, the PUFA/SFA and Hypocholesterolaemic/Hypercholesterolaemic (HH) ratios increased in both fried and microwaved trout, whereas significant increases in ω3/ω6 as well as EPA + DHA/C16 content were observed only in microwaved samples. A significant increase in energy content was observed in all cooked samples, whereas the cholesterol decreased. Research results show that microwaving is recommended as the best cooking method for a healthy consumption of rainbow trout.