Freshly extracted juice from two different varieties of an under-utilized fruit (Syzygium malaccense) was subjected to various non-thermal treatments, such as ultrasonication (5 and 10 min at 50% amplitude with 30 s pulse lap time) and ozonation (0.1 ppm for 20 min), along with the standard heat treatment (85 degrees C/10 min). Various treatment's effect on the microbiological, physicochemical, and bioactive constituents of the juice were studied throughout storage (28 days at 4 degrees C). Ultrasonication treatment enhanced the bioactive components retention, and higher vitamin C, TPC, DPPH, and ABTS radical scavenging activities were observed in ultrasonicated (5 min) juices compared to others. The ozone treatment showed deleterious effects on wax apple juice, reducing TPC, vitamin C, and flavonoids. Organic acid profiling revealed ascorbic, malic, fumaric, and tartaric acids; major phenolic compounds included catechin, rutin, syringic, vanillic, protocatechuic, gallic, and rosmarinic acids in the fruit juice. Pearson correlation coefficient highlighted positive correlations between these compounds and antioxidant activity in both juices. The present study addresses the scarcity of information on wax apple juice constituents, highlighting its rich organic acids and phenolics content. The results showed that ultrasonication (5 min) treatment emerged as an alternative to thermal treatment, preserving bioactive compounds in wax apple juice.