The selection and diffusion in the poultry sector of hybrid breeds able to produce higher amount of meat and eggs, led over time to the erosion of genetic resources. One of the strategies that can be applied in order to stem such phenomenon, concerns the valorization of the animal products, meat or eggs, obtained from indigenous poultry breeds. Therefore, the aim of this study is to characterize the qualitative aspects of eggs obtained from the Nera Atriana hen, an Italian indigenous laying hen characteristic of the Abruzzo region, making a direct comparison with a commercial hybrid reared in the same environment and applying the same feeding protocol. The trial was conducted for a period of 5 months (from March to July 2019), in which 6 egg samplings were performed (one at the beginning and additional 5 on a monthly basis); each sampling involved the collection of 15 eggs per group of animals for a total of 90 eggs per genotype. Eggs were specifically subjected to evaluations of the physical parameters, including the yolk color, and analyses aimed at determining the content of total lipids, cholesterol, and β-carotene. In addition to this, the fatty acids profile and the electrophoretic pattern of the globular proteins of the yolk were characterized. Eggs from hybrid hens were characterized by higher total weight with significantly higher values specifically associated to albumen and yolk weight and to the albumen percentage. In the eggs obtained from the local hen, higher relative percentages were instead found in the quantity of shell and yolk; furthermore, in the same samples was observed a higher yolk redness, a cholesterol concentration tending to be lower although not significant (p = 0.0521), and a greater amount of saturated fatty acids which could justify a lower susceptibility of the food to oxidative processes following transformation with heat treatments. With regard to the fatty acid composition, differences were specifically observed for palmitic (C16:0) and palmitoleic (C16:1 cis-9) acids that showed higher relative percentages in eggs from local breed, and for the oleic acid (C18:1 cis-9) which was more represented in eggs from commercial hens. In conclusion, some interesting nutritional features, in a preliminary way, have been highlighted that could lead the consumer to prefer these “niche” products over those obtained from commercial hybrids.