A new type of fruit wine made from red dragon fruit juice was produced through alcoholic fermentation (AF) with different yeasts: Saccharomyces cerevisiae EC-1118, Torulaspora delbrueckii Biodiva and Lachancea thermotolerans Concerto. Complete AF with similar fermentation rates in terms of sugar utilisation and ethanol production (8–9%, v/v) was achieved by three yeast strains. T. delbrueckii produced a significantly lower amount of glycerol and acetic acid, while L. thermotolerans produced more lactic and succinic acids. In addition, the two non-Saccharomyces strains were more efficient in proline utilisation. For volatile compounds, S. cerevisiae produced the highest amounts of esters, while T. delbrueckii produced more higher alcohols, isoamyl acetate and terpenes. On the other hand, AF caused significant degradation of betacyanin pigments and total phenolic compounds. Nevertheless, better retention of antioxidant activity and colour stability was found in L. thermotolerans and T. delbrueckii fermented wines than that of S. cerevisiae. This study suggested that it is feasible to use pure non-Saccharomyces yeast to produce red dragon fruit wine for commercialization.