Phenolics, in addition to color, flavor, nutritional value, and organoleptic properties, are mainly responsible for the oxidative stability of olive oil and change according to the degree of maturity and processes. In this study, it was aimed to optimize the malaxation process using the response surface method in terms of oil yield and bioactive constituents, including total phenolic content, ortho-diphenol, and free radical scavenging activity of olive oils at three maturity stages. At all maturity stages, malaxation temperature and time were effective on the considered responses. The total phenolic content, ortho-diphenols, and free radical scavenging activity of the oil samples varied in a range of 86.11–338.94 (milligram gallic acid equivalent (GAE)/kg), 66.74–154.88 (mg GAE/kg), and 42.49–90.10%, respectively, depending on the malaxation conditions. Tyrosol, hydroxytyrosol, vanillic acid, vanillin, p-coumaric acid, ferulic acid, quercetin, and luteolin were the individual phenolics determined chromatographically in the olive oil samples, and their amounts varied to different extents depending on the malaxation conditions and maturity stages. The models show high predictive performance to explain the variation in the study. The optimum conditions for malaxation temperature and time for oil extraction from spotted, purple, and black fruits were 35 °C/45 min, 33 °C/44 min, and 35 °C/24 min, respectively.