Selenium is an essential micronutrient with significant antioxidant activity promising in mitigating the formation of acrylamide during high-temperature roasting. In this study, green coffee beans pretreated with selenium (Se-coffee) were investigated on their selenium uptake, selenium retention in green and roasted beans, antioxidant activities, and formation of acrylamide during conventional and superheated steam roasting. Comparisons were made with positive (pretreated without selenium) and negative (untreated) controls. The acrylamide formation was significantly inhibited in Se-coffee (108.9–165.3 μg/kg) compared to the positive and negative controls by 73.9% and 52.8%, respectively. The reduction of acrylamide by superheated steam roasting only observed in the untreated coffee beans (negative control) by 32.4% parallel to the increase in its antioxidant activity. Selenium pretreatment significantly increased antioxidant activity of the roasted Se-coffee beans after roasting although soaking pretreatment significantly reduced antioxidant activity in the green beans. Acrylamide reduction in the roasted coffee beans strongly correlated with the change in antioxidant capacities after roasting (∆FRAP, 0.858; ∆DPPH, 0.836). The results indicate that the antioxidant properties of the organic selenium suppressed acrylamide formation during coffee roasting.