The growing demand for eggs from alternative housing systems is driven by perceived nutritional and welfare benefits. However, the trade-off between enhanced bioactive composition and exposure to environmental contaminants remains insufficiently explored. This study evaluated the physical traits, bioactive compounds, and heavy metal content of 480 commercially available table eggs from four housing systems: organic, free-range, barn, and enriched cages. Organic eggs exhibited the highest albumen quality, expressed by Haugh units (92.03 vs. 70.86 in cages) and lysozyme activity (144,877 U/mL vs. 119,830 U/mL in cages), alongside the highest concentrations of fat-soluble vitamins (e.g., vitamin A at 1600 μg/100 g and vitamin E at 3267 μg/100 g) and n-3 polyunsaturated fatty acids, including docosahexaenoic acid (DHA: 0.673% vs. 0.360% in cages). Conversely, organic eggs presented the weakest eggshells (breaking strength of 34.19 N vs. 47.05 N in cages) and a less favourable lipid profile regarding atherogenicity (AI: 0.411) and thrombogenicity (TI: 3.455) indices. Crucially, organic eggs contained significantly higher levels of lead (0.361 mg/kg) compared to indoor systems (0.041 mg/kg in barn and 0.102 mg/kg in cages), highlighting their susceptibility to environmental pollution. Cage and barn eggs were associated with higher chemical safety and shell strength but demonstrated a lower overall bioactive value. Ultimately, the choice of table eggs may involve a trade-off between the health-promoting benefits of extensive systems and the potential risks of heavy metal contamination, emphasising the need for integrated food safety management.