Juices from the Chilean-grown maqui berry (Aristotelia chilensis) were fermented using two yeasts, Saccharomyces cerevisiae bayanus EC 118 (EC) and Saccharomyces cerevisiae cerevisiae RC 212 (RC), to investigate changes in phenolic phytochemical profile, antioxidant capacity, and anti-inflammatory potential. RC and EC fermentations both stabilized juice pH and reduced sugar content by 67% and 78% within 3 days, respectively. Initial concentrations of delphinidin 3-sambubioside-5-glucoside (41.0%), a major anthocyanin, were elevated up to 56.7% or 60.0% in EC or RC treatments, respectively, by day 9 of fermentation. Delphinidin 3, 5-diglucoside decreased from 24.5% to 9.5% (EC treatment) or to 8.6% (RC treatment) by day 9. Total polyphenol, proanthocyanidin, and hydrolysable tannins decreased over time in all treatments. Fermentation significantly increased gallic acid (a product of tannin hydrolysis) in EC treatment. Antioxidant capacity was enhanced with both yeasts, and EC fermented juice was able to inhibit iNOS and COX-2 protein expression at significantly lower concentrations compared to the unfermented juice. These results suggest that yeast fermentation changes polyphenolic composition in maqui juice in ways that could potentially improve health beneficial properties.