The objective of this work was to evaluate the influence of diets containing different lipid sources on eggs quality during refrigerated storage, on yolk fatty acid composition, and on cholesterol in the yolk. Four diets were used containing Soy Oil (SO), Sunflower Seed (SS), and Meat and Bone Meal + Soy Oil (MBM + SO) or Meat and Bone Meal + Tallow (MBM + TA). The experiment followed a factorial design 4 × 3 with four dietary treatments and three storage times. The eggs were stored at 4 °C for 0, 30, and 60 days. The collected eggs were analyzed for egg weight loss, Haugh units, yolk moisture, yolk lipid oxidation, and cooked yolk firmness. Refrigerated storage reduced Haugh units, and increased yolk moisture. Sixty days of storage time reduced the firmness of hard-cooked yolk. There was an interaction between dietary treatment and storage time for egg weight loss and lipid oxidation. With regard to yolk fatty acid profile, MBM + TA diet increased the contents of palmitic and palmitoleic acids. The levels of oleic and arachidonic acids were higher in yolks from birds fed with SS diet. Linoleic acid level was higher in the yolk from treatment with SO diet. Diets containing MBM + SO induced higher levels of docosahexaenoic acid. Yolk cholesterol content was reduced with the inclusion of SS in the diet. Therefore, the type of lipid present in the diet and refrigerated storage for 60 days at 4 °C can affect the egg quality.