Traditionally antioxidant activity of melanoidins has only been evaluated in food for implication in shelf life but gastrointestinal digestion is necessary to study their potential bioactivity. In addition, the biological fate of melanoidins has been stressed during the past decade since they did not behave as inert substances. In the present paper a soluble coffee melanoidin isolated from brewed coffee after ultrafiltration with a 10 kDa cutoff membrane was treated ionically and enzymatically collecting the respective high and low molecular weight fractions. Antioxidant activity of these fractions was evaluated with five well-described assays (DPPH, ABTS, ORAC, HOSC, and FRAP) that were previously setup in a plate reader based automatized analysis. Low molecular weight compounds released from melanoidin after gastrointestinal digestion exerted the highest antioxidant activity, even higher than compounds bound ionically to melanoidins. Gastrointestinal digestion is able to modify coffee melanoidins to some extent, as hypothesized from their absolute antioxidant activities. Two options are plausible: by modifying/releasing the ionically bound compounds and/or by genesis of new more active structures from the melanoidin skeleton after enzymatic treatment.