Alperujo, an antioxidant-rich by-product of olive oil extraction, could protect β-cells against oxidative damage. Our goal was to study the antioxidant effects of an alperujo extract (AE) on MIN6 β-cells challenged with glucose or hydrogen peroxide. MIN6 β-cells were challenged with glucose (100 mM) or H2O2 (0.15 mM), with or without AE (20 μM phenol). Reactive oxygen species, intracellular iron (Fe), insulin, glucose uptake, and mRNA gene expression of Uncoupling Protein-2 (UCP-2), Thioredoxin (TRDX), p47phox, and the ratio Bax/Bcl-2 were measured. ROS increased when the stressors were incubated with AE (p < 0.05 and p < 0.01, respectively). Intracellular Fe increased in glucose presence (100 mM p < 0.001). Insulin secretion improved when cells were pre-incubated with AE (p < 0.001) and glucose uptake increased when cells were pre-incubated with AE for 3 days and then further treated with glucose (p < 0.001). After 3 days of AE alone, mRNA relative expression of UCP-2 and TRDX increased (p < 0.001) and after 5 days p47phox, also increased. The Bax/Bcl-2 ratio tended to decrease in the samples pre-incubated with AE. The Alperujo extract, in vitro, had a pro-oxidant behavior, however pre-incubating MIN6 β-cells with AE tended to protect them against apoptosis, thereby enhancing insulin secretion.