Due to limited fish meal and fish oil resources and their high costs for the aquaculture industry, it is necessary to find alternative sustainable sources of protein and lipids. Therefore, seven different diets were formulated with different levels of animal by-products, vegetable proteins, fish oil and rapeseed oil, to feed farmed Atlantic salmon, and their effects on growth performance, muscle lipid class, and fatty acid composition were examined. Protein sources included anchovy, poultry, feather, blood, corn, soy and wheat. Growth performance indicated that the diet with the lowest fish meal and fish oil content resulted in the lowest weight gain and final weight, followed by the diet containing the highest level of animal by-products. The lipid class analysis showed no statistical difference in the muscle total lipid content using different diets. However, significant statistical differences were observed among the main lipid classes; triacylglycerols, phospholipids, and sterols. The diet containing 1.4% omega-3 long-chain fatty acids resulted in the highest content of triacylglycerols and phospholipids. Diets containing medium and low levels of fish oil and fish meal, respectively, led to as high a level of ω3 fatty acids in muscle as when fish were fed diets with high levels of fish meal and fish oil. The results of this study suggest that feeding a diet containing low levels of fish meal and moderate levels of fish oil does not significantly affect ω3 fatty acid composition in muscle. Fish meal could be reduced to 5% without affecting growth as long as there was a minimum of 5% fish oil, and animal by-products did not exceed 26% of the diet.