Fruit juice, a popular beverage, is prone to spoilage due to its high moisture and nutritional content, which may pose health risks to consumers. This study aims to evaluate the changes in physicochemical and microbiological qualities of rock melon juice (RMJ) subjected to two pasteurization methods: mild-temperature-short-time (MTST) pasteurization at 70°C for 30 s and high-temperature-short-time (HTST) pasteurization at 85°C for 20 s. The juice was stored at 4°C for 21 days, with total soluble solids (TSS), titratable acidity (TA), pH, TSS/TA ratio, colour, total plate count (TPC), and yeast and mold counts assessed on days 1, 7, 14, and 21. Results indicated that pasteurization significantly affected (p < 0.05) the physicochemical and microbiological qualities of RMJ, except for TSS, TA, and pH. On day 1, both treatments increased the L* value (control: 68.16, MTST: 69.50, HTST: 69.70) while reducing a* (control: 20.15, MTST: 16.84, HTST: 15.87) and b* (control: 51.14, MTST: 46.67, HTST: 46.96) values, resulting in a lighter juice colour due to pigment degradation. MTST and HTST samples showed lower TPC (2.15 and 2.00 log CFU/mL) compared to the control sample (3.96 log CFU/mL) on day 1. During 21 days of storage, the microbial loads of pasteurized RMJ were observed at 2 log CFU/mL and lower. No significant differences (p > 0.05) were observed in TSS, TA, and microbiological quality between MTST- and HTST-treated RMJ after storage. HTST pasteurization is recommended to minimize colour changes, potentially enhancing juice acceptability and marketability.