The ability to trace the origin of eggs from backyard-raised hens is important due to their higher market value compared to barn-raised eggs. This study aimed to differentiate eggs from these two rearing systems using isotopic, elemental, and fatty acid profiles of egg yolks. A total of 90 egg yolk samples were analyzed, analytical results being followed by statistical tests (Student’s t-test) showing significant differences in δ18O, several elements (Mg, K, Sc, Mn, Fe, Ni, Cu, Zn, As, Cd, Ba, Pb), and fatty acids compositions (C23:0, C17:0, C18:0, C16:1n7, C18:1n9, C18:2n6, C20:1n7, C20:4n6, C20:5n3, C22:6n3), as well as in the ratios of SFA, PUFA, and UFA. The results indicated a nutritional advantage in backyard eggs due to their lower n-6 polyunsaturated fatty acid content and a more favorable n-6 to n-3 ratio, linked to differences in the hens’ diet and rearing systems. To classify the production system (backyard vs. barn), three pattern recognition methods were applied: linear discriminant analysis (LDA), k–nearest neighbor (k–NN), and multilayer perceptron artificial neural networks (MLP–ANN). LDA provided perfect initial separation, achieving 98.9% accuracy in cross-validation. k-NN yielded classification rates of 98.4% for the training set and 85.7% for the test set, while MLP–ANN achieved 100% accuracy in training and 92.3% in testing, with minor misclassification. These results demonstrate the effectiveness of fusion among isotopic, elemental, and fatty acid profiles in distinguishing backyard eggs from barn eggs and highlight the nutritional benefits of the backyard-rearing system.