Orange, lemon, and lime by-products emerge as promising sources of phenolic compounds. This study presents the first comprehensive assessment of the antioxidant capacity and food safety considerations of citrus pomace, aiming for their safe integration into the food industry. Results reveal that lemon and lime by-products are particularly rich in eriocitrin, hesperidin, trans-ferulic acid, and p-coumaric acid, significantly contributing to their antioxidant capacity. Regarding food safety, none of the nine regulated mycotoxins were detected. However, heavy metals were present below the maximum levels. Furthermore, pesticide residues were present, although at low levels in most cases. Contrarily, lime by-product presented high levels of the flutriafol. This study highlights the value of citrus by-products as source of natural antioxidants and emphasizes the necessity of monitoring and mitigating pesticide residues for their safe incorporation into functional food products. These findings support the sustainable utilization of citrus pomace within the circular economy framework, offering opportunities for innovation in the food industry.