Three commercial samples consisting of enriched calcium-free caseinophosphopeptides (CPP), enriched calcium-bound caseinophosphopeptides (Ca-CPP) and an enzymatically hydrolyzed casein (hCN) were in vitro digested according to COST-Infogest protocol. As assessed by UPLC-HR-MS/MS, the digests contained 207–235 unique caseinophosphopeptides, and the species presenting the cluster sssEE were more abundant in CPP digest. The antioxidant activity at three different doses of each digest was firstly evaluated on human intestinal Caco-2/HT-29 70/30 co-culture. In presence of AAPH, hCN and CPP digests displayed a dose-dependent antioxidant activity equal or even greater than Vitamin C. In presence of Fe2+, the digests exerted an antioxidant activity mainly at the highest dose. Antioxidant activities of the intestinal metabolized digests was then evaluated on human osteoblast (Saos-2) cells. The digests exerted an antioxidant activity in presence of AAPH, but not in presence of Fe2+. These results highlight milk-derived peptides as potential dietary supplements for gut and bone health.