Most of the eggs for consumption are produced in a conventional housing system although the demand for organic eggs is increasing because consumers assume better nutritional characteristics. This study was conducted to compare the quality of organic eggs and enriched cage eggs. A total of 409 organic eggs and 385 eggs from hens housed in enriched cages were directly collected from 15 different farms, located in Spain and were analyzed within 4 days after laying. The differences in quality by removing the time bias that can be caused by marketing time were thus determined. All the hens were of three different lines, 47–50 weeks old and consumed commercial feed with the same nutritional composition. The quality traits evaluated were egg weight (EW g), egg shape index (SI), shell thickness (ST), shell percentage (SP), Haugh units (HU), dense albumen percentage (DAP), total albumen percentage (TAP), yolk color (YC), yolk percentage (YP), Roche scale (RS), moisture (M), ash content (AC), total protein (TP), total yolk carotenoids (TYC), total fat (TF), saturated fatty acids (SFA), monounsaturated fatty acids (MFA), and polyunsaturated fatty acids (PFA). Estimates of differences were obtained by generalized least squares using housing system, genetic line and their interaction as factors. Significant differences were observed for EW (65.3 vs 62.9), SI (77.60 vs 76.10), HU (83.60 vs 81.80), TAP (66.5 vs 64.17), YC (3.11 vs 1.89), RS (11.79 vs 9.48), TP (9.99 vs 8.55), TYC (4.188 vs 2.650), SFA (32.20 vs 30.00) and MFA (53.40 vs 44.20) in favor of the enriched cage system. In the organic system, the quality parameters that had higher and significant values were ST (0.34 vs 0.32), SP (10.52 vs 9.41), YP (25.20 vs 24.30), AC (1.12 vs 0.93) and PFA (26.00 vs 14.00). Significant interactions between the housing system and the hen line followed the same pattern observed for fixed effects. Organic eggs were lighter, less rounded with better shell quality and therefore showed lower Haugh unit values and a lower albumen percentage. Total protein, total fat, and lipid profile were within the usual average values for commercial eggs, although the proportion of polyunsaturated fatty acids, which are beneficial for consumers, was higher in organic eggs.